1.
Evolution
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Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of organisation, including the levels of species, individual organisms. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, existing patterns of biodiversity have been shaped both by speciation and by extinction. More than 99 percent of all species that lived on Earth are estimated to be extinct. Estimates of Earths current species range from 10 to 14 million, more recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. In the mid-19th century, Charles Darwin formulated the theory of evolution by natural selection. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are fitted for the functional roles they perform. The processes by which the changes occur, from one generation to another, are called evolutionary processes or mechanisms, the four most widely recognized evolutionary processes are natural selection, genetic drift, mutation and gene migration. Natural selection and genetic drift sort variation, mutation and gene migration create variation, consequences of selection can include meiotic drive, nonrandom mating and genetic hitchhiking. In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwins theory of evolution by natural selection through the discipline of population genetics, the importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis, evolutionism, evolutionary computation, a sub-field of artificial intelligence, involves the application of Darwinian principles to problems in computer science. The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander, such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura, in contrast to these materialistic views, Aristotelianism considered all natural things as actualisations of fixed natural possibilities, known as forms. This was part of a teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. In the 17th century, the new method of modern science rejected the Aristotelian approach, however, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognized the nature of species relationships. Other naturalists of this time speculated on the change of species over time according to natural laws
2.
Introduction to evolution
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Evolution is the process of change in all forms of life over generations, and evolutionary biology is the study of how evolution occurs. Biological populations evolve through changes that correspond to changes in the organisms observable traits. Genetic changes include mutations, which are caused by damage or replication errors in an organisms DNA, the age of the Earth is about 4.54 billion years. There are microbial mat found in 3.48 billion-year-old sandstone discovered in Western Australia. According to one of the researchers, If life arose relatively quickly on Earth, then it could be common in the universe. More than 99 percent of all species, amounting to five billion species. Estimates on the number of Earths current species range from 10 million to 14 million, of which about 1.2 million have been documented and over 86 percent have not yet been described. More recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. Evolution does not attempt to explain the origin of life, all individuals have hereditary material in the form of genes that are received from their parents, then passed on to any offspring. Among offspring there are variations of genes due to the introduction of new genes via random changes called mutations or via reshuffling of existing genes during sexual reproduction, the offspring differs from the parent in minor random ways. If those differences are helpful, the offspring is more likely to survive and this means that more offspring in the next generation will have that helpful difference and individuals will not have equal chances of reproductive success. In this way, traits that result in organisms being better adapted to their living conditions become more common in descendant populations and these differences accumulate resulting in changes within the population. This process is responsible for the diverse life forms in the world. The forces of evolution are most evident when populations become isolated, over time, isolated populations can branch off into new species. The majority of genetic mutations neither assist, change the appearance of, through the process of genetic drift, these mutated genes are neutrally sorted among populations and survive across generations by chance alone. In contrast to genetic drift, natural selection is not a process because it acts on traits that are necessary for survival. Natural selection and random genetic drift are constant and dynamic parts of life, the modern understanding of evolution began with the 1859 publication of Charles Darwins On the Origin of Species. In addition, Gregor Mendels work with plants helped to explain the patterns of genetics
3.
Evidence of common descent
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Additionally, this evidence supports the modern evolutionary synthesis—the current scientific theory that explains how and why life changes over time. Evolutionary biologists document evidence of descent by developing testable predictions, testing hypotheses. Additional genetic information conclusively supports the relatedness of life and has allowed scientists to develop phylogenetic trees and it has also led to the development of molecular clock techniques to date taxon divergence times and to calibrate these with the fossil record. Fossils are important for estimating when various lineages developed in geologic time, vestigial structures and comparisons in embryonic development are largely a contributing factor in anatomical resemblance in concordance with common descent. Since metabolic processes do not leave fossils, research into the evolution of the cellular processes is done largely by comparison of existing organisms physiology. Many lineages diverged at different stages of development, so it is possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor and this is especially obvious in the field of insular biogeography. The development and spread of resistant bacteria provides evidence that evolution due to natural selection is an ongoing process in the natural world. Natural selection is ubiquitous in all research pertaining to evolution, taking note of the fact all of the following examples in each section of the article document the process. Alongside this are observed instances of the separation of populations of species into sets of new species, speciation has been observed directly and indirectly in the lab and in nature. Multiple forms of such have been described and documented as examples for individual modes of speciation, one of the strongest evidences for common descent comes from the study of gene sequences. Comparative sequence analysis examines the relationship between the DNA sequences of different species, producing several lines of evidence that confirm Darwins original hypothesis of common descent. If the hypothesis of common descent is true, then species that share a common ancestor inherited that ancestors DNA sequence, more closely related species have a greater fraction of identical sequence and shared substitutions compared to more distantly related species. The simplest and most powerful evidence is provided by phylogenetic reconstruction, such reconstructions, especially when done using slowly evolving protein sequences, are often quite robust and can be used to reconstruct a great deal of the evolutionary history of modern organisms. These reconstructed phylogenies recapitulate the relationships established through morphological and biochemical studies, while a minority of these elements might later be found to harbor function, in aggregate they demonstrate that identity must be the product of common descent rather than common function. All known extant organisms are based on the biochemical processes, genetic information encoded as nucleic acid, transcribed into RNA. Perhaps most tellingly, the Genetic Code is the same for almost every organism, ATP is used as energy currency by all extant life. A deeper understanding of developmental biology shows that morphology is, in fact. Another noteworthy example is the vertebrate body plan, whose structure is controlled by the homeobox family of genes
4.
Common descent
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Common descent describes how, in evolutionary biology, a group of organisms share a most recent common ancestor. There is evidence of descent that all life on Earth is descended from the last universal common ancestor. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all living on Earth. Common ancestry between organisms of different species arises during speciation, in new species are established from a single ancestral population. Organisms which share a more recent common ancestor are more closely related, the most recent common ancestor of all currently living organisms is the last universal ancestor, which lived about 3.9 billion years ago. Chance, one might say, turned out a vast number of individuals, a much greater number showed neither adaptation nor order, these last have all perished. Thus the species which we see today are but a part of all those that a blind destiny has produced. In 1790, Immanuel Kant wrote in Kritik der Urteilskraft that the analogy of animal forms implies a common original type, furthermore, the genetic code is nearly identical for all known lifeforms, from bacteria and archaea to animals and plants. The universality of this code is generally regarded by biologists as definitive evidence in favor of the theory of common descent. Analysis of the differences in the genetic code has also provided support for universal common descent. An example would be Cytochrome c which most organisms actually share, a statistical comparison of various alternative hypotheses has shown that universal common ancestry is significantly more probable than models involving multiple origins. Similarities which have no adaptive relevance cannot be explained by convergent evolution, such evidence has come from two areas, amino acid sequences and DNA sequences. Proteins with the same three-dimensional structure need not have identical amino acid sequences, in certain cases, there are several codons that code for the same amino acid. Thus, if two species use the same codon at the place to specify an amino acid that can be represented by more than one codon. The universality of many aspects of life is often pointed to as supportive evidence to the more compelling evidence listed above. These similarities include the energy carrier adenosine triphosphate, and the fact that all amino acids found in proteins are left-handed. It is, however, possible that these similarities resulted because of the laws of physics and chemistry, rather than common descent. Another important piece of evidence is that it is possible to construct detailed phylogenetic trees mapping out the proposed divisions and it should be noted, however, that the formal test was criticised for not including consideration of convergent evolution, and Theobald has defended the method against this claim
5.
Population genetics
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Julian Huxley invented the term in his 1942 book, Evolution, The Modern Synthesis. The modern synthesis solved difficulties and confusions caused by the specialisation, at its heart was the question of whether Mendelian genetics could be reconciled with gradual evolution by means of natural selection. A second issue was whether the changes of macroevolution seen by palaeontologists could be explained by changes seen in the microevolution of local populations. The synthesis included evidence from geneticists who studied populations in the field and these studies were crucial to evolutionary theory. The synthesis drew together ideas from several branches of biology which had separated, particularly genetics, cytology, systematics, botany. The modern synthesis of the early 20th century bridged the gap between the work of geneticists and naturalists, and paleontologists. It states that, All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms, Evolution is gradual, small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongst species are explained as originating gradually through geographical separation and extinction and this theory contrasts with the saltation theory of William Bateson. Natural selection is by far the main mechanism of change, even slight advantages are important when continued, the object of selection is the phenotype in its surrounding environment. The role of genetic drift is equivocal, though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained. Thinking in terms of populations, rather than individuals, is primary, in palaeontology, the ability to explain historical observations by extrapolation from microevolution to macroevolution is proposed. Historical contingency means explanations at different levels may exist, gradualism does not mean constant rate of change. The idea that speciation occurs after populations are reproductively isolated has been much debated, in plants, polyploidy must be included in any view of speciation. Formulations such as evolution consists primarily of changes in the frequencies of alleles between one generation and another were proposed rather later. The traditional view is that biology played little part in the synthesis. In the 19th and early 20th centuries, variations of Lamarckism, orthogenesis, also, Darwin did not offer a precise explanation of how new species arise. Weismann and Wallace rejected the Lamarckian idea of inheritance of acquired characteristics, weismann was translated into English, and though he was influential, it took many years for the full significance of his work to be appreciated. Gregor Mendels work was re-discovered by Hugo de Vries and Carl Correns in 1900, news of this reached William Bateson in England, who reported on the paper during a presentation to the Royal Horticultural Society in May 1900
6.
Genetic variation
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Genetic variation means that biological systems – individuals and populations – are different over space. Each gene pool includes various alleles of genes, the variation occurs both within and among populations, supported by individual carriers of the variant genes. Genetic variation is brought about, fundamentally, by mutation, which is a permanent change in the structure of chromosomes. Genetic recombination also produces changes within alleles, Genetic variation among individuals within a population can be identified at a variety of levels. It is possible to identify genetic variation from observations of variation in either quantitative traits or discrete traits. Genetic variation can also be identified by examining variation at the level of enzymes using the process of protein electrophoresis, polymorphic genes have more than one allele at each locus. Half of the genes code for enzymes in insects and plants may be polymorphic. Ultimately, genetic variation is caused by variation in the order of bases in the nucleotides in genes, New technology now allows scientists to directly sequence DNA which has identified even more genetic variation than was previously detected by protein electrophoresis. Examination of DNA has shown variation in both coding regions and in the non-coding intron region of genes. Geographic variation means genetic differences in populations from different locations and this is caused by natural selection or genetic drift. Genetic variation within a population is measured as the percentage of gene loci that are polymorphic or the percentage of gene loci in individuals that are heterozygous. Random mutations are the source of genetic variation. Mutations are likely to be rare and most mutations are neutral or deleterious, polyploidy is an example of chromosomal mutation. Polyploidy is a condition wherein organisms have three or more sets of genetic variation, crossing over and random segregation during meiosis can result in the production of new alleles or new combinations of alleles. Furthermore, random fertilization also contributes to variation, Variation and recombination can be facilitated by transposable genetic elements, endogenous retroviruses, LINEs, SINEs, etc. For a given genome of an organism, genetic variation may be acquired in somatic cells or inherited through the germline. Genetic variation can be divided into different forms according to the size, small-scale sequence variation includes base-pair substitution and indels. Large-scale Structural variation can be either copy number variation, or chromosomal rearrangement, numerical variation in whole chromosomes or genomes can be either polyploidy or aneuploidy
7.
Genetic diversity
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Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary, genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals, the academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions, diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common and this occurs in host–pathogen interactions, where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele. According to the researcher in the study, Dr. Richard Lankau, If any one type is removed from the system, the cycle can break down. The interdependence between genetic and species diversity is delicate, changes in species diversity lead to changes in the environment, leading to adaptation of the remaining species. Changes in genetic diversity, such as in loss of species, loss of genetic diversity in domestic animal populations has also been studied and attributed to the extension of markets and economic globalization. Genetic diversity plays an important role in the survival and adaptability of a species, variation in the populations gene pool provides variable traits among the individuals of that population. These variable traits can be selected for, via natural selection, ultimately leading to a change in the population. Genetic diversity is essential for a species to evolve, with very little gene variation within the species, healthy reproduction becomes increasingly difficult, and offspring are more likely to have problems resulting from inbreeding. The vulnerability of a population to certain types of diseases can also increase with reduction in genetic diversity, concerns about genetic diversity are especially important with large mammals due to their small population size and high levels of human-caused population effects. When humans initially started farming, they used selective breeding to pass on traits of the crops while omitting the undesirable ones. Selective breeding leads to monocultures, entire farms of nearly genetically identical plants, If the genetic variation that the bacterium is best at attacking happens to be that which humans have selectively bred to use for harvest, the entire crop will be wiped out. A very similar occurrence is the cause of the infamous Potato Famine in Ireland, in the 1840s, much of Irelands population depended on potatoes for food
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Mutation
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In biology, a mutation is the permanent alteration of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal DNA or other genetic elements. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements, mutations may or may not produce discernible changes in the observable characteristics of an organism. Mutations play a part in normal and abnormal biological processes including, evolution, cancer, and the development of the immune system. The genomes of RNA viruses are based on RNA rather than DNA, the RNA viral genome can be double stranded or single stranded. In some of these viruses replication occurs quickly and there are no mechanisms to check the genome for accuracy and this error-prone process often results in mutations. Mutation can result in different types of change in sequences. Mutations in genes can either have no effect, alter the product of a gene, mutations can also occur in nongenic regions. Mutations can involve the duplication of large sections of DNA, usually through genetic recombination and these duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of shared ancestry, known as homology. Here, protein domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the eye uses four genes to make structures that sense light. Another advantage of duplicating a gene is that this increases engineering redundancy, other types of mutation occasionally create new genes from previously noncoding DNA. Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, in the Homininae, two fused to produce human chromosome 2, this fusion did not occur in the lineage of the other apes. Sequences of DNA that can move about the genome, such as transposons, make up a fraction of the genetic material of plants and animals. For example, more than a million copies of the Alu sequence are present in the genome. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes, nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation. The abundance of some changes within the gene pool can be reduced by natural selection, while other more favorable mutations may accumulate
9.
Natural selection
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Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in heritable traits of a population over time, Charles Darwin popularised the term natural selection, and compared it with artificial selection. Variation exists within all populations of organisms and this occurs partly because random mutations arise in the genome of an individual organism, and offspring can inherit such mutations. Throughout the lives of the individuals, their genomes interact with their environments to cause variations in traits, the environment of a genome includes the molecular biology in the cell, other cells, other individuals, populations, species, as well as the abiotic environment. Individuals with certain variants of the trait may survive and reproduce more than individuals with other, less successful, variants, therefore, factors that affect reproductive success are also important, including sexual selection and fecundity selection. Over time, this process can result in populations that specialise for particular ecological niches, in other words, natural selection is a key process in the evolution of a population. Natural selection can be contrasted with artificial selection, in which humans intentionally choose specific traits, Natural selection is one of the cornerstones of modern biology. The concept of natural selection originally developed in the absence of a theory of heredity, at the time of Darwins writing. The union of traditional Darwinian evolution with subsequent discoveries in classical genetics formed the synthesis of the mid-20th century. The addition of molecular genetics has led to developmental biology. While genotypes can slowly change by random genetic drift, natural selection remains the primary explanation for adaptive evolution, empedocles idea that organisms arose entirely by the incidental workings of causes such as heat and cold was criticised by Aristotle in Book II of Physics. He posited natural teleology in its place, and believed that form was achieved for a purpose, nevertheless, he accepted in his biology that new types of animals, monstrosities, can occur in very rare instances. And in like manner as to the parts in which there appears to exist an adaptation to an end. Yet it is impossible that this should be the true view, for teeth and all other natural things either invariably or normally come about in a given way, but of not one of the results of chance or spontaneity is this true. We do not ascribe to chance or mere coincidence the frequency of rain in winter, but frequent rain in summer we do, nor heat in the dog-days, therefore action for an end is present in things which come to be and are by nature. The struggle for existence was later described by the Islamic writer Al-Jahiz in the 9th century, the classical arguments were reintroduced in the 18th century by Pierre Louis Maupertuis and others, including Darwins grandfather, Erasmus Darwin. Until the early 19th century, the view in Western societies was that differences between individuals of a species were uninteresting departures from their Platonic ideals of created kinds. However, the theory of uniformitarianism in geology promoted the idea that simple and this theory, Lamarckism, was an influence on the Soviet biologist Trofim Lysenkos antagonism to mainstream genetic theory as late as the mid 20th century
10.
Adaptation
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In biology, an adaptation, also called an adaptive trait, is a trait with a current functional role in the life of an organism that is maintained and evolved by means of natural selection. Adaptation refers to both the current state of being adapted and to the evolutionary process that leads to the adaptation. Adaptations enhance the fitness and survival of individuals, organisms face a succession of environmental challenges as they grow and develop and are equipped with an adaptive plasticity as the phenotype of traits develop in response to the imposed conditions. The developmental norm of reaction for any given trait is essential to the correction of adaptation as it affords a kind of insurance or resilience to varying environments. Adaptation is, first of all, a process, to rather be with the animal, an internal parasite can illustrate the distinction, such a parasite may have a very simple bodily structure, but nevertheless the organism is highly adapted to its specific environment. From this we see that adaptation is not just a matter of visible traits, in such parasites critical adaptations take place in the life cycle, however, as a practical term, adaptation often refers to a product, those features of a species which result from the process. Many aspects of an animal or plant can be correctly called adaptations, by using the term adaptation for the evolutionary process, and adaptive trait for the bodily part or function, one may distinguish the two different senses of the word. Adaptation is one of the two processes that explain the diverse species found in biology, such as the different species of Darwins finches. The other process is speciation, caused by geographical isolation or some other mechanism, a favorite example used today to study the interplay of adaptation and speciation is the evolution of cichlid fish in African lakes, where the question of reproductive isolation is much more complex. Adaptation is not always a simple matter where the ideal phenotype evolves for an external environment. An organism must be viable at all stages of its development and this places constraints on the evolution of development, behavior and structure of organisms. However, it is not clear what relatively small should mean, the origin of eukaryotic symbiosis exemplifies a more dramatic example. All adaptations help organisms survive in their ecological niches, the adaptive traits may be structural, behavioral or physiological. Structural adaptations are features of an organism. Behavioral adaptations are composed of inherited behavior chains and/or the ability to learn, behaviors may be inherited in detail, examples, searching for food, mating, vocalizations. Adaptation, then, affects all aspects of the life of an organism, the following definitions are mainly due to Theodosius Dobzhansky. Adaptation is the process whereby an organism becomes better able to live in its habitat or habitats. Adaptedness is the state of being adapted, the degree to which an organism is able to live, an adaptive trait is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing
11.
Polymorphism (biology)
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Polymorphism in biology and zoology is the occurrence of two or more clearly different morphs or forms, also referred to as alternative phenotypes, in the population of a species. In order to be classified as such, morphs must occupy the same habitat at the same time, three mechanisms may cause polymorphism, Genetic polymorphism - where the phenotype of each individual is genetically determined. A conditional development strategy, where the phenotype of each individual is set by environmental cues, a mixed development strategy, where the phenotype is randomly assigned during development. Polymorphism as used in zoology and biology involves morphs of the phenotype, polymorphism is common in nature, it is related to biodiversity, genetic variation and adaptation, it usually functions to retain variety of form in a population living in a varied environment. The most common example is sexual dimorphism, which occurs in many organisms, other examples are mimetic forms of butterflies, and human hemoglobin and blood types. According to the theory of evolution, polymorphism results from evolutionary processes and it is heritable and is modified by natural selection. In polyphenism, an individuals genetic make-up allows for different morphs, in genetic polymorphism, the genetic make-up determines the morph. Ants exhibit both types in a single population, polymorphism also refers to the occurrence of structurally and functionally more than two different types of individuals, called zooids within the same organism. It is a feature of Cnidarians. Although in general use polymorphism is quite a broad term, in biology it has given a specific meaning, being distinguishable from monomorphism. A more specific term, when there are two forms, is dimorphism. The term omits characters showing continuous variation, even though this has a heritable component, polymorphism deals with forms in which the variation is discrete or strongly bimodal or polymodal. Morphs must occupy the same habitat at the time, this excludes geographical races. The use of the words morph or polymorphism for what is a different geographical race or variant is common. The significance of geographical variation is in that it may lead to allopatric speciation, the term was first used to describe visible forms, but nowadays it has been extended to include cryptic morphs, for instance blood types, which can be revealed by a test. Rare variations are not classified as polymorphisms, and mutations by themselves do not constitute polymorphisms, to qualify as a polymorphism there has to be some kind of balance between morphs underpinned by inheritance. The criterion is that the frequency of the least common morph is too high simply to be the result of new mutations or, as a rough guide, polymorphism crosses several discipline boundaries, including ecology and genetics, evolution theory, taxonomy, cytology and biochemistry. Different disciplines may give the same concept different names, and different concepts may be given the same name, for example, there are the terms established in ecological genetics by E. B
12.
Genetic drift
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Genetic drift is the change in the frequency of a gene variant in a population due to random sampling of organisms. The alleles in the offspring are a sample of those in the parents, a populations allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation, when there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. In the early 20th century, vigorous debates occurred over the importance of natural selection versus neutral processes. The process of genetic drift can be illustrated using 20 marbles in a jar to represent 20 organisms in a population, consider this jar of marbles as the starting population. Half of the marbles in the jar are red and half blue, in each new generation the organisms reproduce at random. To represent this reproduction, randomly select a marble from the original jar, repeat this process until there are 20 new marbles in the second jar. The second jar then contains a second generation of offspring, consisting of 20 marbles of various colours, unless the second jar contains exactly 10 red marbles and 10 blue marbles, a random shift occurred in the allele frequencies. Repeat this process a number of times, randomly reproducing each generation of marbles to form the next, the numbers of red and blue marbles picked each generation fluctuates, sometimes more red and sometimes more blue. This fluctuation is analogous to genetic drift – a change in the allele frequency resulting from a random variation in the distribution of alleles from one generation to the next. It is even possible that in any one generation no marbles of a particular colour are chosen, in this example, if no red marbles are selected, the jar representing the new generation contains only blue offspring. If this happens, the red allele has been lost permanently in the population, while the remaining blue allele has become fixed, in small populations, fixation can occur in just a few generations. The mechanisms of genetic drift can be illustrated with a simplified example, consider a very large colony of bacteria isolated in a drop of solution. The bacteria are genetically identical except for a gene with two alleles labeled A and B. A and B are neutral alleles meaning that they do not affect the ability to survive and reproduce, all bacteria in this colony are equally likely to survive. Suppose that half the bacteria have allele A and the other half have allele B, thus A and B each have allele frequency 1/2. The drop of solution then shrinks until it has enough food to sustain four bacteria. All other bacteria die without reproducing, among the four who survive, there are sixteen possible combinations for the A and B alleles
13.
Gene flow
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In population genetics, gene flow is the transfer of alleles or genes from one population to another. Migration into or out of a population may be responsible for a change in allele frequencies. Immigration may also result in the addition of new variants to the established gene pool of a particular species or population. There are a number of factors affect the rate of gene flow between different populations. One of the most significant factors is mobility, as greater mobility of an individual tends to give it greater migratory potential, animals tend to be more mobile than plants, although pollen and seeds may be carried great distances by animals or wind. Maintained gene flow between two populations can lead to a combination of the two gene pools, reducing the genetic differentiation between the two groups. For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other, physical barriers to gene flow are usually, but not always, natural. They may include mountain ranges, oceans, or vast deserts. In some cases, they can be artificial, man-made barriers, such as the Great Wall of China and this is because Ulmus pumila has wind-pollination as its primary means of propagation and the latter-plants carry out pollination through insects. Samples of the species which grow on either side have been shown to have developed genetic differences. Barriers to gene flow need not always be physical, species can live in the same environment, yet show very limited gene flow due to limited hybridization or hybridization yielding unfit hybrids. Female choice can also play a role in hindering gene flow, males in the northern population respond strongly to the local male songs but relatively weakly to the nonlocal songs of southern males. In contrast, southern males respond equally to both local and nonlocal songs, a barrier to gene flow exists from South to North as a result of the female preference. Horizontal gene transfer is the transfer of genes between organisms, either through hybridization, antigenic shift, or reassortment is sometimes an important source of genetic variation, viruses can transfer genes between species. Bacteria can incorporate genes from other bacteria, exchange genes with living bacteria. Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic domains, thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes. Biologist Gogarten suggests the original metaphor of a no longer fits the data from recent genome research. Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT, each contemporary molecule has its own history and traces back to an individual molecule cenancestor
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Speciation
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Speciation is the evolutionary process by which biological populations evolve to become distinct species. The biologist Orator F. Cook coined the term speciation in 1906 for the splitting of lineages or cladogenesis, Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book The Origin of Species. He also identified sexual selection as a mechanism, but found it problematic. There are four modes of speciation in nature, based on the extent to which speciating populations are isolated from one another, allopatric, peripatric, parapatric. Speciation may also be induced artificially, through animal husbandry, agriculture, whether genetic drift is a minor or major contributor to speciation is the subject matter of much ongoing discussion. All forms of speciation have taken place over the course of evolution, however. During allopatric speciation, a population splits into two isolated populations. When the populations come back into contact, they have evolved such that they are isolated and are no longer capable of exchanging genes. Island genetics is the associated with the tendency of small. Examples include insular dwarfism and the changes among certain famous island chains. The Galápagos Islands are particularly famous for their influence on Charles Darwin, though the finches were less important for Darwin, more recent research has shown the birds now known as Darwins finches to be a classic case of adaptive evolutionary radiation. In peripatric speciation, a subform of allopatric speciation, new species are formed in isolated and it is related to the concept of a founder effect, since small populations often undergo bottlenecks. Genetic drift is often proposed to play a significant role in peripatric speciation, parapatric speciation may be associated with differential landscape-dependent selection. Even if there is a gene flow between two populations, strong differential selection may impede assimilation and different species may eventually develop, habitat differences may be more important in the development of reproductive isolation than the isolation time. Ecologists refer to parapatric and peripatric speciation in terms of ecological niches, a niche must be available in order for a new species to be successful. Ring species such as Larus gulls have been claimed to illustrate speciation in progress, the grass Anthoxanthum odoratum may be starting parapatric speciation in areas of mine contamination. Sympatric speciation refers to the formation of two or more descendant species from an ancestral species all occupying the same geographic location. Often-cited examples of sympatric speciation are found in insects that become dependent on different host plants in the same area, however, the existence of sympatric speciation as a mechanism of speciation remains highly debated
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Adaptive radiation
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Starting with a recent single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits. An example of radiation would be the avian species of the Hawaiian honeycreepers. Via natural selection, these birds adapted rapidly and converged based on the different environments of the Hawaiian islands, much research has been done on adaptive radiation due to its dramatic effects on the diversity of a population. However, more research is needed, especially to fully understand the factors affecting adaptive radiation. Both empirical and theoretical approaches are helpful, though each has its disadvantages, in order to procure the largest amount of data, empirical and theoretical approaches must be united. Four features can be used to identify an adaptive radiation, A common ancestry of component species, note that this is not the same as a monophyly in which all descendants of a common ancestor are included. A phenotype-environment correlation, a significant association between environments and the morphological and physiological traits used to exploit those environments, trait utility, the performance or fitness advantages of trait values in their corresponding environments. Rapid speciation, presence of one or more bursts in the emergence of new species around the time that ecological, the evolution of a novel feature may permit a clade to diversify by making new areas of morphospace accessible. A classic example is the evolution of a cusp in the mammalian tooth. This trait permits a vast increase in the range of foodstuffs which can be fed on, evolution of this character has thus increased the number of ecological niches available to mammals. The trait arose a number of times in different groups during the Cenozoic, birds find other ways to provide for each other, i. e. the evolution of flight opened new avenues for evolution to explore, initiating an adaptive radiation. Other examples include placental gestation, or bipedal locomotion, one famous example where adaptive radiation is seen is with Darwins finches. It has been observed by many evolutionary biologists that fragmented landscapes are often a prime location for adaptive radiation to occur, the differences in geography throughout disjointed landscapes such as islands are believed to promote such diversification. The first obvious explanation for these differences is allopatric speciation, speciation that occurs when populations of the species become isolated geographically. Because the finches are divided amongst the islands, the birds have been evolving separately for several million years, however, this does not account for the fact that many of the species occur in sympatry, with seven or more species inhabiting the same island. This raises the question as to why these species split when living in the environment with all the same resources. Petren, Grant, Grant, and Keller proposed that the speciation of the finches occurred in two parts, an initial, easily observable allopatric event followed by a less clear sympatric event and this sympatric event which occurred second was adaptive radiation. This occurred largely to promote specialization upon each island, one major morphological difference among species sharing one island is beak size and shape
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Co-operation (evolution)
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Co-operation in evolution is the process where groups of organisms work or act together for common or mutual benefits. It is commonly defined as any adaptation that has evolved, at least in part, for example, territorial choruses by male lions discourage intruders and are likely to benefit all contributors. This process contrasts with intragroup competition where individuals work against each other for selfish reasons, cooperation exists not only in humans but in other animals as well. The diversity of taxa that exhibits cooperation is quite large, ranging from zebra herds to pied babblers to African elephants, many animal and plant species cooperate with both members of their own species and with members of other species. Cooperation in animals appears to occur mostly between relatives, spending time and resources assisting a related individual may at first seem destructive to an organisms chances of survival but is actually beneficial over the long-term. However, some researchers, such as ecology professor Tim Clutton-Brock and they state that helpers may receive more direct, and less indirect, gains from assisting others than is commonly reported. These gains include protection from predation and increased reproductive fitness, furthermore, they insist that cooperation may not solely be an interaction between two individuals but may be part of the broader goal of unifying populations. For example, when a ground squirrel sounds an alarm call to other group members of a nearby coyote, it draws attention to itself. There have been multiple hypotheses for the evolution of cooperation, all of which are rooted in Hamiltons models based on inclusive fitness and these models hypothesize that cooperation is favored by natural selection due to either direct fitness benefits or indirect fitness benefits. As explained below, direct benefits encompass by-product benefits and enforced reciprocity, while indirect benefits encompass limited dispersal, kin discrimination, one specific form of cooperation in animals is kin selection, which involves animals promoting the reproductive success of their kin, thereby promoting their own fitness. Different theories explaining kin selection have been proposed, including the pay-to-stay, the pay-to-stay theory suggests that individuals help others rear offspring in order to return the favor of the breeders allowing them to live on their land. The territory inheritance theory contends that individuals help in order to have improved access to breeding areas once the breeders depart, studies conducted on red wolves support previous researchers contention that helpers obtain both immediate and long-term gains from cooperative breeding. Researchers evaluated the consequences of red wolves decisions to stay with their packs for extended periods of time after birth, while delayed dispersal helped other wolves offspring, studies also found that it extended male helper wolves life spans. This suggests that kin selection may not only benefit an individual in the long-term through increased fitness, some research suggests that individuals provide more help to closer relatives. This phenomenon is known as kin discrimination and they found that different species exhibited varying degrees of kin discrimination, with the largest frequencies occurring among those who have the most to gain from cooperative interactions. Cooperation exists not only in animals but also in plants, in a greenhouse experiment with Ipomoea hederacea, a climbing plant, results show that kin groups have higher efficiency rates in growth than non-kin groups do. This is expected to rise out of reduced competition within the kin groups, the inclusive fitness theory provides a good overview of possible solutions to the fundamental problem of cooperation, its contradiction to natural selection. Direct benefits can result from simple by-product of cooperation or enforcement mechanisms and this is also called mutually beneficial cooperation as both actor and recipient depend on direct fitness benefits, which are broken down into two different types, by-product benefit and enforcement
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Coevolution
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In biology, coevolution occurs when two or more species reciprocally affect each others evolution. Charles Darwin mentioned evolutionary interactions between flowering plants and insects in On the Origin of Species, the term coevolution was coined by Paul R. Ehrlich and Peter H. Raven in 1964. Each party in a coevolutionary relationship exerts selective pressures on the other, Coevolution includes many forms of mutualism, host-parasite, and predator-prey relationships between species, as well as competition within or between species. In many cases, the selective pressures drive an evolutionary arms race between the species involved, Coevolution is primarily a biological concept, but researchers have applied it by analogy to fields such as computer science, sociology, and astronomy. Coevolution is evident in the development of relationships between many pairs of organisms, and serving a wide variety of types of mutual benefit. Each fig species has its own fig wasp which pollinates the fig, nevertheless, some ant species can exploit trees without reciprocating, and hence have been given various names such as cheaters, exploiters, robbers and freeloaders. Although cheater ants do important damage to the organs of trees, their net effect on host fitness is difficult to forecast. He first mentioned coevolution as a possibility in On the Origin of Species, modern insect-pollinated flowers are conspicuously coadapted with insects to ensure pollination and in return to reward the pollinators with nectar and pollen. The two groups have coevolved for over 100 million years, creating a network of interactions. Either they evolved together, or at some later stages they came together, likely with pre-adaptations, the term coevolution was coined by Paul R. Ehrlich and Peter H. Raven in 1964, to describe the evolutionary interactions of plants and butterflies. Several highly successful insect groups—especially the Hymenoptera and Lepidoptera as well as types of Diptera and Coleoptera —evolved in conjunction with flowering plants during the Cretaceous. However, a group of wasps sister to the bees evolved at the time as flowering plants. At least three aspects of flowers appear to have coevolved between flowering plants and insects, because they involve communication between these organisms. Firstly, flowers communicate with their pollinators by scent, insects use this scent to determine how far away a flower is, to approach it, thirdly, flowers such as some orchids mimic females of particular insects, deceiving males into pseudocopulation. The yucca, Yucca whipplei, is pollinated exclusively by Tegeticula maculata, the moth eats the seeds of the plant, while gathering pollen. The pollen has evolved to become sticky, and remains on the mouth parts when the moth moves to the next flower. The yucca provides a place for the moth to lay its eggs, hummingbirds and ornithophilous flowers have evolved a mutualistic relationship. The flowers have nectar suited to the diet, their color suits the birds vision
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Divergent evolution
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Divergent evolution is the accumulation of differences between groups, leading to the formation of new species. The term can also be applied in molecular biology characteristics, such as to proteins that derive from two or more homologous genes, both orthologous genes and paralogous genes can be said to display divergent evolution. Because of the latter, it is possible for divergent evolution to occur between two genes within a species, similarities between species that have diverged is due to their common origin, so such similarities are homologies. In contrast, convergent evolution arises when an adaptation has arisen independently, creating structures such as the wings of birds. Divergent evolution similarly split the lineage from chimpanzees. Darwins finches provide an example of divergent evolution, where some 15 species diverged from a single species of finch that arrived on the Galapagos islands. The divergent evolution of wolves and domesticated dogs from an ancestor, perhaps the grey wolf. Recent studies of the mitochondrial DNA of wolves and of domesticated dogs have found great divergence while also supporting the hypothesis that dogs descend from wolves. Speciation, the divergence of one species into two or more descendant species, occurs when a part of the species is separated from the population by a reproductive barrier. In allopatric and peripatric speciation, the barrier is the result of a physical barrier. Once separated, the species begins to adapt to their new environment via genetic drift, after many generations and continual evolution, the populations become unable to interbreed with one another. Adaptive radiation Cladistics Devolution Molecular evolution
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Convergent evolution
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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 an example, as flying insects, birds. Functionally similar features that have arisen through convergent evolution are analogous, whereas homologous structures or traits have a common origin, 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 but different from parallel evolution. Many instances of convergent evolution are known in plants, including the development of C4 photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals. In morphology, analogous traits arise when different species live in similar ways and/or a similar environment, when occupying similar ecological niches similar problems can lead to similar solutions. The British anatomist Richard Owen was the first to identify the difference between analogies and homologies. In biochemistry, physical and chemical constraints on mechanisms have caused some active site arrangements such as the triad to evolve independently in separate enzyme superfamilies. In his 1989 book Wonderful Life, Stephen Jay Gould argued that if one could rewind the tape of life the same conditions were encountered again, evolution could take a very different course. In cladistics, a homoplasy is a trait shared by two or more taxa for any other than that they share a common ancestry. Taxa which do share ancestry are part of the same clade, homoplastic traits caused by convergence are therefore, from the point of view of cladistics, confounding factors which could lead to an incorrect analysis. In some cases, it is difficult to tell whether a trait has been lost and then re-evolved convergently, or whether a gene has simply been switched off, such a re-emerged trait is called an atavism. From a mathematical standpoint, a gene has a steadily decreasing probability of retaining potential functionality over time. When two species are similar in a character, evolution is defined as parallel if the ancestors were also similar. When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly specified, the enzymology of proteases provides some of the clearest examples of convergent evolution. These examples reflect the intrinsic chemical constraints on enzymes, leading evolution to converge on equivalent solutions independently and repeatedly, serine and cysteine proteases use different amino acid functional groups as a nucleophile. In order to activate that nucleophile, they orient an acidic, the chemical and physical constraints on enzyme catalysis have caused identical triad arrangements to evolve independently more than 20 times in different enzyme superfamilies
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Parallel evolution
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Parallel evolution is the development of a similar trait in related, but distinct, species descending from the same ancestor, but from different clades. However the criteria for defining convergent as opposed to parallel evolution often are unclear in practice, however, this distinction is not clear-cut. For one thing, the conditions are partly a matter of degree. Some scientists accordingly have argued that evolution and convergent evolution are more or less indistinguishable. Others insist that in practice we should not shy away from the area because many important distinctions between parallel and convergent evolution remain. When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly specified and that period of separation would have permitted the accumulation of many relevant differences. Stephen Jay Gould differed, he described some of the examples as having started from the common ancestor of all marsupials and placentals. In contrast, where quite different structures clearly have been co-opted to a form and function. For example, consider Mixotricha paradoxa, a microbe which has assembled a system of rows of apparent cilia. However, on inspection it turns out that in Mixotricha paradoxa, what appear to be cilia actually are smaller symbiont microorganisms, the definition of a trait is crucial in deciding whether a change is seen as divergent, or as parallel or convergent. A similar situation occurs considering the homology of morphological structures, for example, many insects possess two pairs of flying wings. In beetles, the first pair of wings is hardened into elytra, wing covers with little role in flight, similar to convergent evolution, evolutionary relay describes how independent species acquire similar characteristics through their evolution in similar ecosystems, but not at the same time, such as. Colouration that serves as a warning to predators and for mating displays has evolved in different species. In the plant kingdom, the most familiar examples of evolution are the forms of leaves. Some extinct archosaurs evolved an upright posture and likely were warm-blooded and these two characteristics are also found in most mammals. Interestingly, modern crocodiles have a four chambered heart and a crurotarsal, the extinct pterosaurs and the birds both evolved wings as well as a distinct beak, but not from a recent common ancestor. Internal fertilization has evolved independently in sharks, some amphibians and amniotes, the patagium is a fleshy membrane that is found in gliding mammals such as flying lemurs, flying squirrels, sugar gliders and the extinct Volaticotherium. These mammals all acquired the patagium independently, pyrotherians evolved a body plan similar to proboscideans
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Extinction
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In biology and ecology, extinction is the end of an organism or of a group of organisms, normally a species. The moment of extinction is considered to be the death of the last individual of the species, although the capacity to breed. Because a species range may be very large, determining this moment is difficult. This difficulty leads to such as Lazarus taxa, where a species presumed extinct abruptly reappears after a period of apparent absence. More than 99 percent of all species, amounting to five billion species. Estimates on the number of Earths current species range from 10 million to 14 million, of which about 1.2 million have been documented and over 86 percent have not yet been described. More recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described, the relationship between animals and their ecological niches has been firmly established. Mass extinctions are relatively rare events, however, isolated extinctions are quite common, only recently have extinctions been recorded and scientists have become alarmed at the current high rate of extinctions. Most species that become extinct are never scientifically documented, some scientists estimate that up to half of presently existing plant and animal species may become extinct by 2100. A dagger symbol next to a name is often used to indicate its extinction. A species is extinct when the last existing member dies, Extinction therefore becomes a certainty when there are no surviving individuals that can reproduce and create a new generation. Pinpointing the extinction of a species requires a definition of that species. If it is to be declared extinct, the species in question must be distinguishable from any ancestor or daughter species. Extinction of a plays a key role in the punctuated equilibrium hypothesis of Stephen Jay Gould. In ecology, extinction is often used informally to refer to local extinction, in which a species ceases to exist in the area of study. This phenomenon is known as extirpation. Local extinctions may be followed by a replacement of the species taken from other locations, species which are not extinct are termed extant. Those that are extant but threatened by extinction are referred to as threatened or endangered species, currently an important aspect of extinction is human attempts to preserve critically endangered species
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Abiogenesis
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Abiogenesis, biopoiesis, \by-o-po-ee-sis\ or informally, the origin of life, is the natural process by which life arises from non-living matter, such as simple organic compounds. The study of abiogenesis can be geophysical, chemical, or biological, Life itself is dependent upon the specialized chemistry of carbon and water and is largely based upon five different families of chemicals. Carbohydrates are sugars, and as monomer units can be assembled into polymers called polysaccharides, such as cellulose, nitrogenous bases are organic molecules in which the amine group of nitrogen, combined with two hydrogen atoms, plays an important part. Chlorophyll is based upon a porphyrin ring derived from amine monomer units, nucleic acid monomers are made from a carbohydrate monosaccharide a nitrogenous base and one or more high energy phosphate groups. When joined together they form either the unit of inheritance, the gene, made from DNA or RNA, the monomer unit of a protein is always one of 20 amino acids, comprising an amine group, a hydrocarbon and a carboxylic acid. Through a condensation reaction, in which the acid of one amino acid is linked to the amine of another with removal of a water molecule. Polymers of amino acids are termed proteins and these molecules provide many catalytic metabolic functions for living processes, any successful theory of abiogenesis must explain the origins and interactions of these five classes of molecules. Many approaches to investigate how self-replicating molecules, or their components. It is generally thought that current life on Earth is descended from an RNA world, various external sources of energy that may have triggered these reactions have been proposed, including lightning and radiation. Other approaches focus on understanding how catalysis in chemical systems on the early Earth might have provided the precursor molecules necessary for self-replication. Complex organic molecules have found in the Solar System and in interstellar space. It is speculated that the biochemistry of life may have begun shortly after the Big Bang,13.8 billion years ago, the panspermia hypothesis proposes that life originated outside the Earth, not how life came to be. Nonetheless, Earth remains the place in the Universe known to harbour life. In recent years, there have been a number of discoveries that suggested the earliest appearance of life on Earth was even earlier in time, according to biologist Stephen Blair Hedges, If life arose relatively quickly on Earth … then it could be common in the universe. The Hadean Earth is thought to have had a secondary atmosphere, during its formation, the Earth lost a significant part of its initial mass, with a nucleus of the heavier rocky elements of the protoplanetary disk remaining. As Earth lacked the gravity to hold any molecular hydrogen, this component of the atmosphere would have been rapidly lost during the Hadean period, along with the bulk of the original inert gases. The solution of carbon dioxide in water is thought to have made the slightly acidic. The atmosphere at the time has been characterized as a gigantic and it may have been similar to the mixture of gases released today by volcanoes, which still support some abiotic chemistry
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Evolutionary history of life
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The evolutionary history of life on Earth traces the processes by which living and fossil organisms have evolved since life appeared on the planet, until the present day. Earth formed about 4.5 Ga ago and there is evidence that appeared as early as 4.1 Ga. The similarities between all present-day organisms indicate the presence of an ancestor from which all known species have diverged through the process of evolution. More than 99 percent of all species, amounting to five billion species. More recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described, more recently, in 2015, remains of biotic life were found in 4.1 billion-year-old rocks in Western Australia. In March 2017, researchers reported evidence of possibly the oldest forms of life on Earth, according to biologist Stephen Blair Hedges, If life arose relatively quickly on Earth. Then it could be common in the universe, microbial mats of coexisting bacteria and archaea were the dominant form of life in the early Archean and many of the major steps in early evolution are thought to have taken place within them. The evolution of photosynthesis, around 3.5 Ga, eventually led to a buildup of its product, oxygen, in the atmosphere, leading to the great oxygenation event. The earliest evidence of dates from 1.85 Ga. Later, around 1.7 Ga, multicellular organisms began to appear, however the origin and evolution of sexual reproduction remain a puzzle for biologists though it did evolve from a common ancestor that was a single celled eukaryotic species. Bilateria, animals with a front and a back, appeared by 555 Ma, the earliest land plants date back to around 450 Ma, although evidence suggests that microorganisms formed the earliest terrestrial ecosystems, at least 2.9 Ga. Microorganisms are thought to have paved the way for the inception of land plants in the Phanerozoic, land plants were so successful that they are thought to have contributed to the Late Devonian extinction event. Ediacara biota appear during the Ediacaran period, while vertebrates, along with most other modern phyla originated about 525 Ma during the Cambrian explosion. During the Permian period, synapsids, including the ancestors of mammals, dominated the land, during the recovery from this catastrophe, archosaurs became the most abundant land vertebrates, one archosaur group, the dinosaurs, dominated the Jurassic and Cretaceous periods. After the Cretaceous–Paleogene extinction event 66 Ma killed off the dinosaurs, mammals increased rapidly in size. Such mass extinctions may have accelerated evolution by providing opportunities for new groups of organisms to diversify, the Moon has the same composition as Earths crust but does not contain an iron-rich core like the Earths. Many scientists think that about 40 million years later a body the size of Mars struck the Earth, until 2001, the oldest rocks found on Earth were about 3.8 billion years old, leading scientists to estimate that the Earths surface had been molten until then. Accordingly, they named this part of Earths history the Hadean, however, analysis of zircons formed 4
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Timeline of the evolutionary history of life
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This timeline of the evolutionary history of life represents the current scientific theory outlining the major events during the development of life on planet Earth. In biology, evolution is any change across generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of organization, from kingdoms to species. The similarities between all present day organisms indicate the presence of an ancestor from which all known species, living. More than 99 percent of all species, amounting to five billion species. Estimates on the number of Earths current species range from 10 million to 14 million, of which about 1.2 million have been documented and over 86 percent have not yet been described. Species go extinct constantly as environments change, organisms compete for environmental niches, occasionally biodiversity on the planet takes a hit in the form of a mass extinction in which the extinction rate is much higher than usual. A large extinction event often represents an accumulation of smaller extinction events that take place in a brief period of time. The first known mass extinction in earths history was the Great Oxygenation Event 2.4 billion years ago, the event led to the loss of most of the planets obligate anaerobes. The Holocene extinction event is currently under way, in this timeline, Ma means million years ago, ka means thousand years ago, and ya means years ago. 4000 Ma –2500 Ma 2500 Ma –542 Ma, contains the Palaeoproterozoic, Mesoproterozoic and Neoproterozoic eras. 542 Ma – present The Phanerozoic Eon, literally the period of well-displayed life, marks the appearance in the record of abundant. It is subdivided into three eras, the Paleozoic, Mesozoic and Cenozoic, which are divided by mass extinctions. 542 Ma –251.0 Ma and contains the Cambrian, Ordovician, Silurian, Devonian, Carboniferous, from 251.4 Ma to 66 Ma and containing the Triassic, Jurassic and Cretaceous periods. 66 Ma – present Dawkins, Richard, the Ancestors Tale, A Pilgrimage to the Dawn of Life. Understanding Evolution, your one-stop resource for information on evolution, explore complete phylogenetic tree interactively Brandt, Niel. Houston, TX, The TalkOrigins Foundation, Inc, interactive timeline from Big Bang to present Plant Evolution. Sequence of Plant Evolution The History of Animal Evolution, sequence of Animal Evolution Yeo, Dannel, Drage, Thomas
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Human evolution
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Human evolution from its first separation from the last common ancestor of humans and chimpanzees is characterized by a number of morphological, developmental, physiological, and behavioral changes. The most significant of these adaptations are bipedalism, increased size, lengthened ontogeny. The relationship between these changes is the subject of ongoing debate, other significant morphological changes included the evolution of a power and precision grip, a change first occurring in H. erectus. Bipedalism is the adaptation of the hominin and is considered the main cause behind a suite of skeletal changes shared by all bipedal hominins. The earliest hominin, of presumably primitive bipedalism, is considered to be either Sahelanthropus or Orrorin, Ardipithecus, a full biped, arose somewhat later. The early bipeds eventually evolved into the australopithecines and still later into the genus Homo, There are several theories of the adaptation value of bipedalism. A new study provides support for the hypothesis that walking on two legs, or bipedalism, evolved because it used less energy than quadrupedal knuckle-walking, however, recent studies suggest that bipedality without the ability to use fire would not have allowed global dispersal. This change in gait saw a lengthening of the legs proportionately when compared to the length of the arms, another change is the shape of the big toe. Recent studies suggest that Australopithecines still lived part of the time in trees as a result of maintaining a big toe. This was progressively lost in Habilines, anatomically, the evolution of bipedalism has been accompanied by a large number of skeletal changes, not just to the legs and pelvis, but also to the vertebral column, feet and ankles, and skull. The femur evolved into a more angular position to move the center of gravity toward the geometric center of the body. The knee and ankle joints became increasingly robust to support increased weight. To support the weight on each vertebra in the upright position, the human vertebral column became S-shaped. In the feet the big toe moved into alignment with the toes to help in forward locomotion. The arms and forearms shortened relative to the making it easier to run. The foramen magnum migrated under the skull and more anterior, during human birth, because of the variation in size of the pelvic region, the fetal head must be in a transverse position during entry into the birth canal and rotate about 90 degrees upon exit. The human species developed a much larger brain than that of other primates—typically 1,330 cm3 in modern humans. This pattern of brain increase happened through the pattern of human postnatal brain growth differs from that of other apes
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Phylogenetic tree
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The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics, each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed, Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetic comparative methods. Unrooted trees illustrate only the relatedness of the nodes and do not require the ancestral root to be known or inferred. The idea of a tree of life arose from ancient notions of a progression from lower to higher forms of life. Charles Darwin also produced one of the first illustrations and crucially popularized the notion of a tree in his seminal book The Origin of Species. Over time, species classification has become static and more dynamic. A rooted phylogenetic tree is a tree with a unique node corresponding to the most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from trait data or molecular sequencing, unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred, unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry, both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while a tree, sometimes called a tree shape. The last distinction is the most biologically relevant, it arises because there are places on an unrooted tree to put the root. For labeled bifurcating trees, there are,2 n −2. for n ≥2 total rooted trees and. 2 n −3. for n ≥3 total unrooted trees, among labeled bifurcating trees, the number of unrooted trees with n leaves is equal to the number of rooted trees with n −1 leaves. A dendrogram is a term for the diagrammatic representation of a phylogenetic tree. A cladogram is a phylogenetic tree formed using cladistic methods and this type of tree only represents a branching pattern, i. e. its branch spans do not represent time or relative amount of character change
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Biodiversity
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Biodiversity, a contraction of biological diversity, generally refers to the variety and variability of life on Earth. One of the most widely used definitions defines it in terms of the variability within species and it is a measure of the variety of organisms present in different ecosystems. This can refer to genetic variation, ecosystem variation, or species variation within an area, biome, terrestrial biodiversity tends to be greater near the equator, which seems to be the result of the warm climate and high primary productivity. Biodiversity is not distributed evenly on Earth, and is richest in the tropics and these tropical forest ecosystems cover less than 10 per cent of earths surface, and contain about 90 percent of the worlds species. Marine biodiversity tends to be highest along coasts in the Western Pacific, there are latitudinal gradients in species diversity. Biodiversity generally tends to cluster in hotspots, and has been increasing through time, the number and variety of plants, animals and other organisms that exist is known as biodiversity. It is a component of nature and it ensures the survival of human species by providing food, fuel, shelter, medicines. The richness of biodiversity depends on the conditions and area of the region. All species of plants taken together are known as flora and about 300,000 species of plants are known to date, all species of animals taken together are known as fauna which includes birds, mammals, fish, reptiles, insects, crustaceans, molluscs, etc. Rapid environmental changes typically cause mass extinctions, more than 99 percent of all species, amounting to over five billion species, that ever lived on Earth are estimated to be extinct. Estimates on the number of Earths current species range from 10 million to 14 million, of which about 1.2 million have been documented and over 86 percent have not yet been described. More recently, in May 2016, scientists reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described, the total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037 and weighs 50 billion tonnes. In comparison, the mass of the biosphere has been estimated to be as much as 4 TtC. In July 2016, scientists reported identifying a set of 355 genes from the Last Universal Common Ancestor of all living on Earth. The age of the Earth is about 4.54 billion years old, there are microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia. Other early physical evidence of a substance is graphite in 3.7 billion-year-old meta-sedimentary rocks discovered in Western Greenland. More recently, in 2015, remains of life were found in 4.1 billion-year-old rocks in Western Australia. According to one of the researchers, If life arose relatively quickly on Earth, then it could be common in the universe
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Biogeography
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Biogeography is the study of the distribution of species and ecosystems in geographic space and through time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, isolation, phytogeography is the branch of biogeography that studies the distribution of plants. Zoogeography is the branch that studies distribution of animals, Biogeography is an integrative field of inquiry that unites concepts and information from ecology, evolutionary biology, geology, and physical geography. The short-term interactions within a habitat and species of organisms describe the application of biogeography. Historical biogeography describes the long-term, evolutionary periods of time for broader classifications of organisms, early scientists, beginning with Carl Linnaeus, contributed theories to the contributions of the development of biogeography as a science. Beginning in the century, Europeans explored the world and discovered the biodiversity of life. Linnaeus initiated the ways to classify organisms through his exploration of undiscovered territories, the patterns of species distribution across geographical areas can usually be explained through a combination of historical factors such as, speciation, extinction, continental drift, and glaciation. Through observing the distribution of species, we can see associated variations in sea level, river routes, habitat. Additionally, this science considers the constraints of landmass areas and isolation. As writer David Quammen put it. biogeography does more than ask Which species, and, what is sometimes more crucial, Why not. Modern biogeography often employs the use of Geographic Information Systems, to understand the factors affecting organism distribution, often mathematical models and GIS are employed to solve ecological problems that have a spatial aspect to them. Biogeography is most keenly observed on the worlds islands and these habitats are often much more manageable areas of study because they are more condensed than larger ecosystems on the mainland. They can then apply their understanding to similar but more complex mainland habitats, Islands are very diverse in their biomes, ranging from the tropical to arctic climates. This diversity in habitat allows for a range of species study in different parts of the world. One scientist who recognized the importance of geographic locations was Charles Darwin. Two chapters in On the Origin of Species were devoted to geographical distribution, the first discoveries that contributed to the development of biogeography as a science began in the mid-18th century, as Europeans explored the world and discovered the biodiversity of life. During the 18th century most views on the world were shaped around religion and for many natural theologists, Carl Linnaeus, in the mid-18th century, initiated the ways to classify organisms through his exploration of undiscovered territories. When he noticed that species were not as perpetual as he believed, when Noah’s ark landed on Mount Ararat and the waters receded, the animals dispersed throughout different elevations on the mountain
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Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
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Evolutionary taxonomy
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This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the evolutionary synthesis of the early 1940s. Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy, in that it builds evolutionary trees, evolutionary taxonomy arose as a result of the influence of the theory of evolution on Linnaean taxonomy. The idea was popularised in the English-speaking world by the speculative but widely read Vestiges of the Natural History of Creation, following the appearance of On the Origin of Species, Tree of Life representations became popular in scientific works. In contrast, Chambers had proposed specific hypotheses, the evolution of mammals from marsupials. Following Darwins publication, Thomas Henry Huxley used the fossils of Archaeopteryx, thus, a group of extant animals could be tied to a fossil group. The resulting description, that of giving rise to or being the ancestors of birds. Today, with the advent of modern genomics, scientists in every branch of biology make use of molecular phylogeny to guide their research, one common method is multiple sequence alignment. Cavalier-Smith, G. G. Simpson and Ernst Mayr. are some representative evolutionary taxonomists, efforts in combining modern methods of cladistics, phylogenetics, and DNA analysis with classical views of taxonomy have recently appeared. Certain authors have found that analysis is acceptable scientifically as long as paraphyly at least for certain groups is allowable. Such a stance is promoted in papers by Tod F. Stuessy, a particularly strict form of evolutionary systematics has been presented by Richard H. Zander in a number of papers, but summarized in his Framework for Post-Phylogenetic Systematics. Briefly, Zanders pluralistic systematics is thus, A method that cannot falsify a hypothesis is as unscientific as a hypothesis that cannot be falsified, cladistics generates only trees of shared ancestry, not serial ancestry. Taxa evolving seriatim cannot be dealt with by analyzing shared ancestry with cladistic methods, hypotheses such as adaptive radiation from a single ancestral taxon cannot be falsified with cladistics. Cladistics offers a way to cluster by trait transformations but no tree can be entirely dichotomous. Phylogenetics posits shared ancestral taxa as causal agents for dichotomies yet there is no evidence for the existence of such taxa, additional transformational analysis is needed to infer serial descent. The Besseyan cactus or commagram is the best evolutionary tree for showing both shared and serial ancestry, first, a cladogram or natural key is generated. Generalized ancestral taxa are identified and specialized descendant taxa are noted as coming off the lineage with a line of one color representing the progenitor through time, a Besseyan cactus or commagram is then devised that represents both shared and serial ancestry. Progenitor taxa may have one or more descendant taxa, support measures in terms of Bayes factors may be given, following Zanders method of transformational analysis using decibans
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Cladistics
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Therefore, members of a group are assumed to share a common history and are considered to be closely related. The techniques and nomenclature of cladistics have been applied to other disciplines, Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field. What is now called the cladistic method appeared as early as 1901 with a work by Peter Chalmers Mitchell for birds and subsequently by Robert John Tillyard in 1921, Hennig referred to his own approach as phylogenetic systematics. Phenetics was championed at this time by the numerical taxonomists Peter Sneath and Robert Sokal, originally conceived, if only in essence, by Willi Hennig in a book published in 1950, cladistics did not flourish until its translation into English in 1966. Today, cladistics is the most popular method for constructing phylogenies from morphological, unlike phenetics, cladistics is specifically aimed at reconstructing evolutionary histories. The way for computational phylogenetics was paved by phenetics, a set of commonly used from the 1950s to 1980s. Phenetics did not try to reconstruct phylogenetic trees, rather, it tried to build dendrograms from similarity data, the cladistic method interprets each character state transformation implied by the distribution of shared character states among taxa as a potential piece of evidence for grouping. The outcome of an analysis is a cladogram – a tree-shaped diagram that is interpreted to represent the best hypothesis of phylogenetic relationships. Cladists contend that these models are unjustified, every cladogram is based on a particular dataset analyzed with a particular method. Different datasets and different methods, not to mention violations of the mentioned assumptions, only scientific investigation can show which is more likely to be correct. Since the cladograms provide competing accounts of events, at most one of them is correct. Within the primates, all anthropoids are hypothesized to have had a common ancestor all of whose descendants were anthropoids, the prosimians, on the other hand, form a paraphyletic taxon. When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy, symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by being cold-blooded, whereas birds are warm-blooded, an apomorphy or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature, features that are derived in individual taxa are called autapomorphies. Autapomorphies express nothing about relationships among groups, clades are identified by synapomorphies, for example, the possession of digits that are homologous with those of Homo sapiens is a synapomorphy within the vertebrates. The tetrapods can be singled out as consisting of the first vertebrate with such digits homologous to those of Homo sapiens together with all descendants of this vertebrate and it is therefore inferred to have evolved by convergence or reversal. Both mammals and birds are able to maintain a constant body temperature
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Transitional fossil
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A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. This is especially important where the descendant group is sharply differentiated by gross anatomy and these fossils serve as a reminder that taxonomic divisions are human constructs that have been imposed in hindsight on a continuum of variation. Because of the incompleteness of the record, there is usually no way to know exactly how close a transitional fossil is to the point of divergence. Therefore, it cannot be assumed that transitional fossils are direct ancestors of more recent groups, in 1859, when Charles Darwins On the Origin of Species was first published, the fossil record was poorly known. Indeed, Archaeopteryx was discovered just two later, in 1861, and represents a classic transitional form between dinosaurs and birds. Many more transitional fossils have been discovered since then, and there is now abundant evidence of how all classes of vertebrates are related, specific examples include humans and other primates, tetrapods and fish, and birds and dinosaurs. The term missing link has been used extensively in popular writings on evolution to refer to a perceived gap in the hominid evolutionary record. It is most commonly used to refer to any new transitional fossil finds, scientists, however, do not use the term, as it refers to a pre-evolutionary view of nature. Transitional forms are seen as falling between the groups in terms of anatomy, having a mixture of characteristics from inside and outside the newly branched clade. With the establishment of cladistics in the 1990s, relationships commonly came to be expressed in cladograms that illustrate the branching of the lineages in stick-like figures. The different so-called natural or monophyletic groups form nested units, while in traditional classification tetrapods and fish are seen as two different groups, phylogenetically tetrapods are considered a branch of fish. Thus, with there is no longer a transition between established groups, and the term transitional fossils is a misnomer. Differentiation occurs within groups, represented as branches in the cladogram, such early representatives of a group are usually termed basal taxa or sister taxa, depending on whether the fossil organism belongs to the daughter clade or not. A source of confusion is the notion that a transitional form between two different taxonomic groups must be an ancestor of one or both groups. The difficulty is exacerbated by the fact one of the goals of evolutionary taxonomy is to identify taxa that were ancestors of other taxa. However, it is almost impossible to be sure that any form represented in the record is a direct ancestor of any other. Archaeopteryx is a genus of theropod dinosaur closely related to the birds, similar in shape to a European magpie, with the largest individuals possibly attaining the size of a raven, Archaeopteryx could grow to about 0.5 metres in length. Despite its small size, broad wings, and inferred ability to fly or glide and these features make Archaeopteryx a clear candidate for a transitional fossil between dinosaurs and birds, making it important in the study both of dinosaurs and of the origin of birds
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Extinction event
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An extinction event is a widespread and rapid decrease in the biodiversity on Earth. Such an event is identified by a change in the diversity. It occurs when the rate of extinction increases with respect to the rate of speciation, Extinction occurs at an uneven rate. Based on the record, the background rate of extinctions on Earth is about two to five taxonomic families of marine animals every million years. Marine fossils are used to measure extinction rates because of their superior fossil record. The Great Oxygenation Event was probably the first major extinction event, since the Cambrian explosion five further major mass extinctions have significantly exceeded the background extinction rate. In addition to the five mass extinctions, there are numerous minor ones as well. Mass extinctions seem to be a mainly Phanerozoic phenomenon, with extinction rates low before large complex organisms arose, estimates of the number of major mass extinctions in the last 540 million years range from as few as five to more than twenty. These differences stem from the chosen for describing an extinction event as major. In a landmark paper published in 1982, Jack Sepkoski and David M. Raup identified five mass extinctions, the Big Five cannot be so clearly defined, but rather appear to represent the largest of a relatively smooth continuum of extinction events. Cretaceous–Paleogene extinction event,66 Ma at the Cretaceous -Paleogene transition interval, the event formerly called the Cretaceous-Tertiary or K–T extinction or K-T boundary is now officially named the Cretaceous–Paleogene extinction event. About 17% of all families, 50% of all genera and 75% of all species became extinct, in the seas all the ammonites, plesiosaurs and mosasaurs disappeared and the percentage of sessile animals was reduced to about 33%. All non-avian dinosaurs became extinct during that time, the boundary event was severe with a significant amount of variability in the rate of extinction between and among different clades. Mammals and birds, the latter descended from dinosaurs, emerged as dominant large land animals. Triassic–Jurassic extinction event,201.3 Ma at the Triassic-Jurassic transition, about 23% of all families, 48% of all genera and 70% to 75% of all species became extinct. Most non-dinosaurian archosaurs, most therapsids, and most of the amphibians were eliminated. Non-dinosaurian archosaurs continued to dominate aquatic environments, while non-archosaurian diapsids continued to dominate marine environments, the Temnospondyl lineage of large amphibians also survived until the Cretaceous in Australia. Permian–Triassic extinction event,252 Ma at the Permian-Triassic transition, Earths largest extinction killed 57% of all families, 83% of all genera and 90% to 96% of all species
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History of evolutionary thought
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Evolutionary thought, the conception that species change over time, has roots in antiquity - in the ideas of the ancient Greeks, Romans, and Chinese as well as in medieval Islamic science. Naturalists began to focus on the variability of species, the emergence of paleontology with the concept of extinction further undermined static views of nature, in the early 19th century Jean-Baptiste Lamarck proposed his theory of the transmutation of species, the first fully formed theory of evolution. In 1858 Charles Darwin and Alfred Russel Wallace published a new evolutionary theory, unlike Lamarck, Darwin proposed common descent and a branching tree of life, meaning that two very different species could share a common ancestor. Darwin based his theory on the idea of selection, it synthesized a broad range of evidence from animal husbandry, biogeography, geology, morphology. Before that time most biologists regarded other factors as responsible for evolution, alternatives to natural selection suggested during the eclipse of Darwinism included inheritance of acquired characteristics, an innate drive for change, and sudden large mutations. Paleontology and comparative anatomy allowed more detailed reconstructions of the history of life. After the rise of genetics in the 1950s, the field of molecular evolution developed, based on protein sequences and immunological tests. In the late 20th-century, DNA sequencing led to molecular phylogenetics, in addition, the newly recognized factors of symbiogenesis and horizontal gene transfer introduced yet more complexity into evolutionary theory. Discoveries in evolutionary biology have made a significant impact not just within the branches of biology. Proposals that one type of animal, even humans, could descend from other types of animals, are known to go back to the first pre-Socratic Greek philosophers. He also argued that the first human of the form known today must have been the child of a different type of animal, because man needs prolonged nursing to live. Empedocles, argued that what we call birth and death in animals are just the mingling, Plato was called by biologist Ernst Mayr the great antihero of evolutionism, because he promoted belief in essentialism, which is also referred to as the theory of Forms. This theory holds that each type of object in the observed world is an imperfect manifestation of the ideal. In his Timaeus for example, Plato has a tell a story that the Demiurge created the cosmos and everything in it because, being good. Free from jealousy, He desired that all things should be as like Himself as they could be, the creator created all conceivable forms of life, since. Without them the universe will be incomplete, for it not contain every kind of animal which it ought to contain. This principle of plenitude—the idea that all forms of life are essential to a perfect creation—greatly influenced Christian thought. Aristotles works contain accurate observations, fitted into his own theories of the bodys mechanisms, however, for Charles Singer, Nothing is more remarkable than efforts to the relationships of living things as a scala naturae
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Transmutation of species
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The debate over them was an important stage in the history of evolutionary thought and would influence the subsequent reaction to Darwins theory. Transmutation was one of the commonly used for evolutionary ideas in the 19th century before Charles Darwin published On The Origin of Species. Transmutation had previously used as a term in alchemy to describe the transformation of base metals into gold. Transformation is another word used quite as often as transmutation in this context and these early 19th century evolutionary ideas played an important role in the history of evolutionary thought. The terminology did not settle down until some time after the publication of the Origin of Species. The word evolution was quite a late-comer, it can be seen in Herbert Spencers Social Statics of 1851, and there is at least one earlier example, jean-Baptiste Lamarck proposed a hypothesis on the transmutation of species in Philosophie Zoologique. Lamarck did not believe that all living things shared a common ancestor, rather he believed that simple forms of life were created continuously by spontaneous generation. Lamarck also recognized that species were adapted to their environment and he argued that these changes would be inherited by the next generation and produce slow adaptation to the environment. Grant developed Lamarcks and Erasmus Darwins ideas of transmutation and evolutionism, as a young student Charles Darwin joined Grant in investigations of the life cycle of marine animals. Jamesons course closed with lectures on the Origin of the Species of Animals, in 1844 the Scottish publisher Robert Chambers anonymously published an influential and extremely controversial book of popular science entitled Vestiges of the Natural History of Creation. This book proposed a scenario for the origins of the solar system. It claimed that the record showed a progressive ascent of animals with current animals being branches off a main line that leads progressively to humanity. It implied that the lead to the unfolding of a preordained plan that had been woven into the laws that governed the universe. Darwin himself openly deplored the authors poverty of intellect, and dismissed it as a literary curiosity and it also influenced some younger naturalists, including Alfred Russel Wallace, to take an interest in the idea of transmutation. Ideas about the transmutation of species were associated with the radical materialism of the enlightenment and were greeted with hostility by more conservative thinkers. Cuvier attacked the ideas of Lamarck and Geoffroy Saint-Hilaire, agreeing with Aristotle that species were immutable and he also noted that drawings of animals and animal mummies from Egypt, which were thousands of years old, showed no signs of change when compared with modern animals. The strength of Cuviers arguments and his reputation as a leading scientist helped keep transmutational ideas out of the mainstream for decades. Instead, he advocated a form of creation, in which each species had its centre of creation and was designed for this particular habitat
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Charles Darwin
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Charles Robert Darwin, FRS FRGS FLS FZS was an English naturalist, geologist and biologist, best known for his contributions to the science of evolution. Darwin published his theory of evolution with compelling evidence in his 1859 book On the Origin of Species, by the 1870s, the scientific community and much of the general public had accepted evolution as a fact. In modified form, Darwins scientific discovery is the theory of the life sciences. Darwins early interest in nature led him to neglect his education at the University of Edinburgh, instead. Studies at the University of Cambridge encouraged his passion for natural science, puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin began detailed investigations and in 1838 conceived his theory of natural selection. Although he discussed his ideas with several naturalists, he needed time for extensive research and he was writing up his theory in 1858 when Alfred Russel Wallace sent him an essay that described the same idea, prompting immediate joint publication of both of their theories. Darwins work established evolutionary descent with modification as the dominant scientific explanation of diversification in nature, in 1871 he examined human evolution and sexual selection in The Descent of Man, and Selection in Relation to Sex, followed by The Expression of the Emotions in Man and Animals. His research on plants was published in a series of books, Darwin has been described as one of the most influential figures in human history, and he was honoured by burial in Westminster Abbey. Charles Robert Darwin was born in Shrewsbury, Shropshire, on 12 February 1809, at his familys home and he was the fifth of six children of wealthy society doctor and financier Robert Darwin and Susannah Darwin. He was the grandson of two prominent abolitionists, Erasmus Darwin on his fathers side, and Josiah Wedgwood on his mothers side, both families were largely Unitarian, though the Wedgwoods were adopting Anglicanism. The eight-year-old Charles already had a taste for history and collecting when he joined the day school run by its preacher in 1817. From September 1818, he joined his older brother Erasmus attending the nearby Anglican Shrewsbury School as a boarder and he found lectures dull and surgery distressing, so neglected his studies. He learned taxidermy in around 40 daily hour-long sessions from John Edmonstone, one day, Grant praised Lamarcks evolutionary ideas. Darwin was astonished by Grants audacity, but had recently read similar ideas in his grandfather Erasmus journals, Darwin was rather bored by Robert Jamesons natural-history course, which covered geology - including the debate between Neptunism and Plutonism. He learned the classification of plants, and assisted with work on the collections of the University Museum, as Darwin was unqualified for the Tripos, he joined the ordinary degree course in January 1828. He preferred riding and shooting to studying, when his own exams drew near, Darwin focused on his studies and was delighted by the language and logic of William Paleys Evidences of Christianity. In his final examination in January 1831 Darwin did well, coming out of 178 candidates for the ordinary degree. Darwin had to stay at Cambridge until June 1831, inspired with a burning zeal to contribute, Darwin planned to visit Tenerife with some classmates after graduation to study natural history in the tropics
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On the Origin of Species
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On the Origin of Species, published on 24 November 1859, is a work of scientific literature by Charles Darwin which is considered to be the foundation of evolutionary biology. Darwins book introduced the theory that populations evolve over the course of generations through a process of natural selection. It presented a body of evidence that the diversity of life arose by common descent through a pattern of evolution. Darwin included evidence that he had gathered on the Beagle expedition in the 1830s and his subsequent findings from research, correspondence, various evolutionary ideas had already been proposed to explain new findings in biology. The political and theological implications were intensely debated, but transmutation was not accepted by the scientific mainstream, the book was written for non-specialist readers and attracted widespread interest upon its publication. As Darwin was an eminent scientist, his findings were taken seriously and the evidence he presented generated scientific, philosophical, and religious discussion. The debate over the book contributed to the campaign by T. H. Huxley, during the eclipse of Darwinism from the 1880s to the 1930s, various other mechanisms of evolution were given more credit. Despite periodic fluctuations, populations remain roughly the same size, resources such as food are limited and are relatively stable over time. Individuals in a population significantly from one another. Much of this variation is heritable and this slowly effected process results in populations changing to adapt to their environments, and ultimately, these variations accumulate over time to form new species. In later editions of the book, Darwin traced evolutionary ideas as far back as Aristotle, Nature was widely believed to be unstable and capricious, with monstrous births from union between species, and spontaneous generation of life. After the turmoil of the English Civil War, the Royal Society wanted to show that science did not threaten religious, in Gods benevolent design, carnivores caused mercifully swift death, but the suffering caused by parasitism was a puzzling problem. The biological classification introduced by Carl Linnaeus in 1735 also viewed species as fixed according to the divine plan. In 1766, Georges Buffon suggested that some species, such as horses and asses, or lions, tigers. The Ussher chronology of the 1650s had calculated creation at 4004 BC, wernerians thought strata were deposits from shrinking seas, but James Hutton proposed a self-maintaining infinite cycle, anticipating uniformitarianism. Charles Darwins grandfather Erasmus Darwin outlined a hypothesis of transmutation of species in the 1790s and this process was later called Lamarckism. Lamarck thought there was an inherent progressive tendency driving organisms continuously towards greater complexity, in parallel, Georges Cuvier strongly disputed such ideas, holding that unrelated, fixed species showed similarities that reflected a design for functional needs. His palæontological work in the 1790s had established the reality of extinction, in Britain, William Paleys Natural Theology saw adaptation as evidence of beneficial design by the Creator acting through natural laws
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The eclipse of Darwinism
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Historians of science such as Peter J. There were four major alternatives to natural selection in the late 19th century, the idea that evolution was driven by the inheritance of characteristics acquired during the life of the organism was called neo-Lamarckism. Theistic evolution largely disappeared from the literature by the end of the 19th century as direct appeals to supernatural causes came to be seen as unscientific. Ernst Mayr wrote that as late as 1930 most textbooks still emphasized such non-Darwinian mechanisms, evolution was widely accepted in scientific circles within a few years after the publication of On the Origin of Species, but acceptance of natural selection as its driving mechanism was much less. There were a variety of different factors that motivated people to propose other mechanisms as alternatives to natural selection. Some of these scientists and philosophers, like St. George Jackson Mivart and Charles Lyell, others, such as Herbert Spencer, the botanist George Henslow, and Samuel Butler, felt that evolution was an inherently progressive process that natural selection alone was insufficient to explain. They distrusted the work of naturalists like Darwin and Alfred Russel Wallace, dependent on field observations of variation, adaptation, similarly, Louis Agassiz saw the recapitulation theory as symbolising a pattern of the sequence of creations in which humanity was the goal of a divine plan. In 1844 Vestiges adapted Agassizs concept into theistic evolutionism and its anonymous author Robert Chambers proposed a law of divinely ordered progressive development, with transmutation of species as an extension of recapitulation theory. This popularised the idea, but it was condemned by the scientific establishment. Agassiz remained forcefully opposed to evolution, and after he moved to America in 1846 his idealist argument from design of development became very influential. In 1858 Owen cautiously proposed that development could be a real expression of a continuing creative law. Many of Darwins supporters accepted evolution on the basis that it could be reconciled with design, in particular, Asa Gray considered natural selection to be the main mechanism of evolution and sought to reconcile it with natural theology. By 1872 Darwinism in its sense of the fact of evolution was accepted as a starting point. Around 1890 only a few men held onto the idea of design in science. There was still unease about the implications of natural selection, jean-Baptiste Lamarck had originally proposed a theory on the transmutation of species that was largely based on a progressive drive toward greater complexity. Typically, such characteristics included changes caused by the use or disuse of a particular organ and it was this mechanism of evolutionary adaptation through the inheritance of acquired characteristics that much later came to be known as Lamarckism. They considered Lamarckism to be progressive and thus philosophically superior to Darwins idea of natural selection acting on random variation. In addition, Cope and Haeckel both believed that evolution was a progressive process, the idea of linear progress was an important part of Haeckels recapitulation theory of evolution, which held that the embryological development of an organism repeats its evolutionary history
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History of molecular evolution
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Before the rise of molecular biology in the 1950s and 1960s, a small number of biologists had explored the possibilities of using biochemical differences between species to study evolution. However, it was not until the 1950s that biologists developed techniques for producing biochemical data for the study of molecular evolution. The first molecular systematics research was based on immunological assays and protein fingerprinting methods, beginning in the 1950s, a few naturalists also experimented with molecular approaches—notably Ernst Mayr and Charles Sibley. While such early biochemical techniques found grudging acceptance in the biology community and this would change as molecular biology shed more light on the physical and chemical nature of genes. Crow offered two different explanations based on the paradox first articulated by J. B. S. H. J. Muller dubbed this genetic load, bruce Wallace, working with J. C. King, used the hypothesis to develop the balance position. In that case, heterosis is simply the result of the expression of heterozygote advantage. Debate continued through 1950s, gradually becoming a focus of population genetics. Accordingly, Kimura and his mentor Crow came down on the side of the classical position, thus, the infinite alleles model offered a potential way to decide between the classical and balance positions, if accurate values for the level of heterozygosity could be found. Their two landmark papers, published in 1966, established a significant level of heterozygosity for Drosophila, however, these findings proved difficult to interpret. Most population geneticists rejected the possibility of widespread neutral mutations, explanations that did not involve selection were anathema to mainstream evolutionary biology, while evolutionary biologists were tentatively branching out into molecular biology, molecular biologists were rapidly turning their attention toward evolution. Francis Crick, Charles Sibley and others recognized the potential for using biological sequences to construct phylogenies, by the early 1960s, techniques for protein sequencing had advanced to the point that direct comparison of homologous amino acid sequences was feasible. In 1961, Emanuel Margoliash and his collaborators completed the sequence for horse cytochrome c, between 1962 and 1965, Pauling and Zuckerkandl refined and elaborated this idea, which they dubbed the molecular clock, and Emil L. Smith and Emanuel Margoliash expanded the analysis to cytochrome c. Early molecular clock calculations agreed fairly well with established divergence times based on paleontological evidence, however, the essential idea of the molecular clock—that individual proteins evolve at a regular rate independent of a species morphological evolution—was extremely provocative. From the early 1960s, molecular biology was increasingly seen as a threat to the core of evolutionary biology. Moreover, Pauling, Zuckerkandl, and other molecular biologists were increasingly bold in asserting the significance of informational macromolecules for all biological processes, including evolution. Mayr and Simpson attended many of the conferences where molecular evolution was discussed. Though not directly related to evolution, the mid-1960s also saw the rise of the gene-centered view of evolution
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Evolutionary developmental biology
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The field grew from 19th century beginnings, where embryology faced a mystery, zoologists did not know how embryonic development was controlled at the molecular level. Charles Darwin noted that having similar embryos implied common ancestry, then, recombinant DNA technology at last brought embryology together with molecular genetics. A key early discovery was of homeotic genes that regulate development in a range of eukaryotes. The field is characterised by some key concepts, which took biologists by surprise and these genes are ancient, being highly conserved among phyla, they generate the patterns in time and space which shape the embryo, and ultimately form the body plan of the organism. Another is that species do not differ much in their genes, such as those coding for enzymes. This multiple pleiotropic reuse explains why these genes are highly conserved, new morphological features and ultimately new species are produced by variations in the toolkit, either when genes are expressed in a new pattern, or when toolkit genes acquire additional functions. Another possibility is the Neo-Lamarckian theory that epigenetic changes are later consolidated at gene level, a recapitulation theory of evolutionary development was proposed by Étienne Serres in 1824–26, echoing the 1808 ideas of Johann Friedrich Meckel, which in turn had been hinted at by Aristotle. They argued that the embryos of higher animals went through or recapitulated a series of stages, for example, the brain of a human embryo looked first like that of a fish, then in turn like that of a reptile, bird, and mammal before becoming clearly human. The embryologist Karl Ernst von Baer opposed this, arguing in 1828 that there was no linear sequence as in the chain of being. Von Baer instead recognised four distinct body plans, radiate, like starfish, molluscan, like clams, articulate, like lobsters. Zoologists then largely abandoned recapitulation, though Ernst Haeckel revived it in 1866, from the early 19th century through most of the 20th century, embryology faced a mystery. Charles Darwin argued that a shared embryonic structure implied a common ancestor, 19th century zoology thus converted embryology into an evolutionary science, connecting phylogeny with homologies between the germ layers of embryos. Zoologists including Fritz Müller proposed the use of embryology to discover relationships between taxa. Müller demonstrated that crustaceans shared the Nauplius larva, identifying several parasitic species that had not been recognised as crustaceans. Müller also recognised that natural selection must act on larvae, just as it does on adults, giving the lie to recapitulation and it took a century before these ideas were shown to be correct. But for the century, without molecular evidence, progress stalled. Biologists assumed that an organism was a reflection of its component genes, the genes coded for proteins. Biochemical pathways evolved through mutations in these genes and it was a simple, clear and nearly comprehensive picture, but it did not explain embryology
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Evolutionary biology
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Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth, starting from a single origin of life. These processes include natural selection, common descent, and speciation, the study of evolution is the central unifying concept in biology. Biology can be divided in various ways, one way is by the level of biological organisation, from molecular to cell, organism to population. Another way is by taxonomic group, with such as zoology, ornithology. A third way is by approach, such as biology, theoretical biology, experimental evolution. These alternative ways of dividing up the subject can be combined with evolutionary biology to create subfields like evolutionary ecology, Evolutionary biology, as an academic discipline in its own right, emerged during the period of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1980s that many universities had departments of evolutionary biology, in the United States, many universities have created departments of molecular and cell biology or ecology and evolutionary biology, in place of the older departments of botany and zoology. Palaeontology is often grouped with earth science, microbiology too is becoming an evolutionary discipline, now that microbial physiology and genomics are better understood. The quick generation time of bacteria and viruses such as makes it possible to explore evolutionary questions. Many biologists have contributed to our current understanding of evolution, ford established an empirical research programme. Ronald Fisher, Sewall Wright and J. S. Haldane created a theoretical framework. Ernst Mayr in systematics, George Gaylord Simpson in palaeontology and G. Ledyard Stebbins in botany helped to form the modern synthesis, james Crow, Richard Lewontin, Dan Hartl, Marcus Feldman, and Brian Charlesworth trained a generation of evolutionary biologists. Current research in evolutionary biology covers diverse topics and incorporates ideas from diverse areas, such as molecular genetics, first, some fields of evolutionary research try to explain phenomena that were poorly accounted for in the modern evolutionary synthesis. These include speciation, the evolution of reproduction, the evolution of cooperation, the evolution of ageing. Second, biologists ask the most straightforward evolutionary question, what happened and this includes fields such as palaeobiology, as well as systematics and phylogenetics. Third, the evolutionary synthesis was devised at a time when nobody understood the molecular basis of genes. Today, evolutionary biologists try to determine the architecture of interesting evolutionary phenomena such as adaptation and speciation. They try to reconcile the high heritability seen in studies with the difficulty in finding which genes are responsible for this heritability using genome-wide association studies
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History of paleontology
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The history of paleontology traces the history of the effort to understand the history of life on Earth by studying the fossil record left behind by living organisms. In ancient times Xenophanes, Herodotus, Eratosthenes, and Strabo, the Chinese naturalist Shen Kuo would propose a theory of climate change based on evidence from petrified bamboo. In early modern Europe, the study of fossils emerged as an integral part of the changes in natural philosophy that occurred during the Age of Reason. The expanding knowledge of the record also played an increasing role in the development of geology. This contributed to a increase in knowledge about the history of life on Earth. As knowledge of lifes history continued to improve, it became obvious that there had been some kind of successive order to the development of life. This would encourage early evolutionary theories on the transmutation of species, after Charles Darwin published Origin of Species in 1859, much of the focus of paleontology shifted to understanding evolutionary paths, including human evolution, and evolutionary theory. The last half of the 19th century saw an expansion in paleontological activity. Many transitional fossils have been discovered, and there is now considered to be abundant evidence of how all classes of vertebrates are related, the last few decades of the 20th century saw a renewed interest in mass extinctions and their role in the evolution of life on Earth. There was also a renewed interest in the Cambrian explosion that saw the development of the plans of most animal phyla. The discovery of fossils of the Ediacaran biota and developments in paleobiology extended knowledge about the history of life back far before the Cambrian, leonardo da Vinci, in an unpublished notebook, also concluded that some fossil sea shells were the remains of shellfish. However, in cases, the fossils were complete remains of shellfish species that closely resembled living species. In 1027, the Persian naturalist, Ibn Sina, proposed an explanation of how the stoniness of fossils was caused in The Book of Healing and he modified an idea of Aristotles, which explained it in terms of vaporous exhalations. Ibn Sina modified this into the theory of petrifying fluids, which was elaborated on by Albert of Saxony in the 14th century and was accepted in some form by most naturalists by the 16th century. Shen Kuo of the Song Dynasty used marine fossils found in the Taihang Mountains to infer the existence of geological processes such as geomorphology, conrad Gesner published a 1565 work on fossils that contained one of the first detailed descriptions of such a cabinet and collection. The collection belonged to a member of the network of correspondents that Gesner drew on for his works. These cabinet collections and correspondence networks played an important role in the development of natural philosophy, however, most 16th-century Europeans did not recognize that fossils were the remains of living organisms. The etymology of the word comes from the Latin for things having been dug up
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Applications of evolution
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Evolutionary biology, in particular the understanding of how organisms evolve through natural selection, is an area of science with many practical applications. The evolutionary approach is key to current research in biology that does not set out to study evolution per se. For example, evolutionary thinking is key to life history theory, annotation of genes and their function relies heavily on comparative, that is evolutionary, approaches. The field of developmental biology investigates how developmental processes work by using the comparative method to determine how they evolved. A major technological application of evolution is artificial selection, which is the selection of certain traits in a population of organisms. Humans have used artificial selection for thousands of years in the domestication of plants, more recently, such selection has become a vital part of genetic engineering, with selectable markers such as antibiotic resistance genes being used to manipulate DNA in molecular biology. It is also possible to use repeated rounds of mutation and selection to evolve proteins with particular properties, such as modified enzymes or new antibodies, antibiotic resistance can be a result of point mutations in the pathogen genome at a rate of about 1 in 108 per chromosomal replication. The antibiotic action against the pathogen can be seen as an environmental pressure and they will then pass this trait to their offspring, which will result in a fully resistant colony. Understanding the changes that have occurred during organisms evolution can reveal the genes needed to construct parts of the body, for example, the Mexican tetra is an albino cavefish that lost its eyesight during evolution. This helped identify genes required for vision and pigmentation, such as crystallins, similarly, comparing the genome of the Antarctic icefish, which lacks red blood cells, to close relatives such as the Antarctic rockcod revealed genes needed to make these blood cells. As evolution can produce highly optimised processes and networks, it has applications in computer science. Genetic algorithms in particular became popular through the writing of John Holland, as academic interest grew, dramatic increases in the power of computers allowed practical applications, including the automatic evolution of computer programs. Evolutionary algorithms are now used to solve problems more efficiently than software produced by human designers
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Biosocial criminology
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Biosocial criminology is an interdisciplinary field that aims to explain crime and antisocial behavior by exploring both biological factors and environmental factors. Environment has a significant effect on genetic expression, disadvantaged environments enhance antisocial gene expression, suppress prosocial gene action and prevent the realization of genetic potential. The heritability coefficient for antisocial behavior is estimated to be between 0.40 and 0.58, another approach is to examine the relationship between neurophysiology and criminality. One example is that measured levels of such as serotonin. Another is that neuroimaging studies give strong evidence that both brain structure and function are involved in criminal behaviors, the limbic system creates emotions such as anger and jealousy that ultimately may cause criminal behavior. The prefrontal cortex is involved in delaying gratification and impulse control, if this balance is shifted in favor of the limbic system this may contribute to criminal behavior. Men can potentially have many children with little effort, women only a few with great effort and this is argued to contribute to males having more variable reproductive success than females. One argued consequence of this is that males are more aggressive, in particular, low-status males may be more likely to remain completely childless. This may explain why males have higher rates than females and why low status. The evolutionary neuroandrogenic theory focuses on the hormone testosterone as a factor influencing aggression and criminality, in most species, males are more aggressive than females. Castration of males usually has an effect on aggressive behavior in males. In humans, males engage in crime and especially violent crime more than females, the involvement in crime usually rises in the early teens to mid teens in correlation with the rise of testosterone levels. Research on the relationship between testosterone and aggression is difficult since the only reliable measurement of brain testosterone is by lumbar puncture, studies therefore have often instead used less reliable measurements from blood or saliva. Some studies support a link between adult criminality and testosterone, although the relationship is modest if examined separately for each sex, a significant link between juvenile delinquency and testosterone levels has not been established. Some studies have also found testosterone to be associated with behaviors or personality traits linked with criminality such as antisocial behavior, many studies have also been done on the relationship between more general aggressive behavior/feelings and testosterone. About half the studies have found a relationship and about half no relationship, many conflicts causing homicides involve status conflicts, protecting reputation, and seemingly trivial insults. Steven Pinker in his book The Blank Slate argues that in non-state societies without a police it was important to have a credible deterrence against aggression. Therefore, it was important to have a reputation for retaliation, Pinker argues that the development of the state and the police have dramatically reduced the level of violence compared to the ancestral environment
listen) is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines biology, computer science, mathematics and statistics to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.
. PMID 22538125.
The dictionary definition of bioinformatics at Wiktionary
Learning materials related to Bioinformatics at Wikiversity
Media related to Bioinformatics at Wikimedia Commons
