Prologue:

Recently, minister of state for human resource development of India said that the Darwinian theory of evolution was scientifically wrong and should not be taught in Indian institutions. Many scientists and students signed a petition calling upon him to withdraw his remarks. Three science academies of India issued a joint statement, pointing out that those remarks had no scientific basis, and that it would be retrogressive to stop the teaching of evolution. Evolution has become bone of contention between science and religion. Creationism is a religious belief that the universe and life originated “from specific acts of divine creation”, as opposed to the scientific conclusion that they came about through natural processes. Every extinct and extant species on earth have resulted from the same evolutionary processes determining the way they are through shaping their morphology, physiology, and behavior. The traits specific for the human species are the result of the same evolutionary processes responsible for any other living creature. From a general evolutionary perspective, humans are consequently no different than any other species on the planet. Previously, the date, nature, and identity of the last common ancestor between modern humans and their closest living relatives were determined on the basis of comparative anatomy of living species and fragmentary fossil remains. Today, molecular genetic data play an increasing role in establishing phylogenetic relatedness between hominoids, the superfamily including all living and extinct ape and human species. Yet even in scientific disciplines, there is a widespread feeling that evolution is a minor issue in biology, irrelevant to modern advances in molecular biology and devoid of application potential. This could not be farther from the reality. Evolutionary biology is not a branch of biology the way immunology or biochemistry are. Rather, it is a unifying conceptual framework within which facts from all of biology get coherently arranged. Biology without evolution would be like chemistry without the knowledge of the periodic table and reaction mechanisms: an arbitrary collection of facts.

‘For a biologist, the alternative to thinking in evolutionary terms is not to think at all’.

— Peter B. Medawar, Nobel Laureate

An evolutionary perspective sheds light on issues of great societal relevance like why and how we age, how epidemics spread and new pathogenic strains arise, how to improve crops and domesticated animals, how to tackle the evolution of multi-drug resistance in bacteria, why nepotism and despotism are so common in human societies, how notions of justice have developed, why the sudden explosion of the so-called “lifestyle diseases”, to cite just a few examples. Understanding evolution helps us solve biological problems.


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Introduction to evolution:

In the simplest sense, evolution means the slow process of change from a simple to a more complex structure. Evolution assumes that all living things are inter-related. Humans are supposed to have developed from some simpler forms. Most of the scientists today accept the basic principle of evolution but they have varying views regarding how evolution has taken place or how far it has gone. The evolution of life began in the oceans. About four hundred million years ago the first land based creatures emerged. Some of these gradually evolved into the large reptiles who were later displaced by mammals. Mammals are warm-blooded creatures having greater capacity to learn from experience than other animals and this capacity has reached its highest development in the human species.

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Contrary to popular opinion, neither the term nor the idea of biological evolution began with Charles Darwin and his foremost work, On the Origin of Species by Means of Natural Selection (1859). Many scholars from the ancient Greek philosophers on had inferred that similar species were descended from a common ancestor. The word “evolution” first appeared in the English language in 1647 in a nonbiological connection, and it became widely used in English for all sorts of progressions from simpler beginnings. The term Darwin most often used to refer to biological evolution was “descent with modification,” which remains a good brief definition of the process today. Evolution, theory in biology postulating that the various types of plants, animals, and other living things on Earth have their origin in other preexisting types and that the distinguishable differences are due to modifications in successive generations. The theory of evolution is one of the fundamental keystones of modern biological theory.

The diversity of the living world is staggering. More than 2 million existing species of organisms have been named and described; many more remain to be discovered—from 10 million to 30 million, according to some estimates. What is impressive is not just the numbers but also the incredible heterogeneity in size, shape, and way of life—from lowly bacteria, measuring less than a thousandth of a millimetre in diameter, to stately sequoias, rising 100 metres (300 feet) above the ground and weighing several thousand tons; from bacteria living in hot springs at temperatures near the boiling point of water to fungi and algae thriving on the ice masses of Antarctica and in saline pools at −23 °C (−9 °F); and from giant tube worms discovered living near hydrothermal vents on the dark ocean floor to spiders and larkspur plants existing on the slopes of Mount Everest more than 6,000 metres (19,700 feet) above sea level.

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The virtually infinite variations on life are the fruit of the evolutionary process. All living creatures are related by descent from common ancestors. Humans and other mammals descend from shrewlike creatures that lived more than 150 million years ago; mammals, birds, reptiles, amphibians, and fishes share as ancestors aquatic worms that lived 600 million years ago; and all plants and animals derive from bacteria-like microorganisms that originated more than 3 billion years ago. Biological evolution is a process of descent with modification. Lineages of organisms change through generations; diversity arises because the lineages that descend from common ancestors diverge through time.

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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 biological organisation, including the levels of species, individual organisms, and molecules. Repeated formation of new species (speciation), change within species (anagenesis), and loss of species (extinction) throughout the evolutionary history of life on Earth are demonstrated by shared sets of morphological and biochemical traits, including shared DNA sequences. These shared traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct a biological “tree of life” based on evolutionary relationships (phylogenetics), using both existing species and fossils. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped both by speciation and by extinction.

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The 19th-century English naturalist Charles Darwin argued that organisms come about by evolution, and he provided a scientific explanation, essentially correct but incomplete, of how evolution occurs and why it is that organisms have features—such as wings, eyes, and kidneys—clearly structured to serve specific functions. Natural selection was the fundamental concept in his explanation. Darwin proposed that evolution could be explained by the differential survival of organisms following their naturally occurring variation—a process he termed “natural selection.” According to this view, the offspring of organisms differ from one another and from their parents in ways that are heritable—that is, they can pass on the differences genetically to their own offspring. Furthermore, organisms in nature typically produce more offspring than can survive and reproduce given the constraints of food, space, and other environmental resources. If a particular off-spring has traits that give it an advantage in a particular environment, that organism will be more likely to survive and pass on those traits. As differences accumulate over generations, populations of organisms diverge from their ancestors. Natural selection occurs because individuals having more-useful traits, such as more-acute vision or swifter legs, survive better and produce more progeny than individuals with less-favourable traits. Thus, in successive generations members of a population are replaced by progeny of parents better adapted to survive and reproduce in the biophysical environment in which natural selection takes place. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are seemingly 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 recognised evolutionary processes are natural selection (including sexual selection), genetic drift, mutation and gene migration due to genetic admixture. In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwin’s theory of evolution by natural selection through the discipline of population genetics. Genetics, a science born in the 20th century, reveals in detail how natural selection works and led to the development of the modern theory of evolution. 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, and other beliefs about innate “progress” within the largest-scale trends in evolution, became obsolete. Beginning in the 1960s, a related scientific discipline, molecular biology, enormously advanced knowledge of biological evolution and made it possible to investigate detailed problems that had seemed completely out of reach only a short time previously—for example, how similar the genes of humans and chimpanzees might be (they differ in about 4 percent of the units that make up the genes).

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Darwin’s original hypothesis has undergone extensive modification and expansion, but the central concepts stand firm. Studies in genetics and molecular biology—fields unknown in Darwin’s time—have explained the occurrence of the hereditary variations that are essential to natural selection. Genetic variations result from changes, or mutations, in the nucleotide sequence of DNA, the molecule that genes are made from. Such changes in DNA now can be detected and described with great precision. Genetic mutations arise by chance. They may or may not equip the organism with better means for surviving in its environment. But if a gene variant improves adaptation to the environment (for example, by allowing an organism to make better use of an available nutrient, or to escape predators more effectively—such as through stronger legs or disguising coloration), the organisms carrying that gene are more likely to survive and reproduce than those without it. Over time, their descendants will tend to increase, changing the average characteristics of the population. Although the genetic variation on which natural selection works is based on random or chance elements, natural selection itself produces “adaptive” change—the very opposite of chance.

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Chance and randomness do factor into evolution and the history of life in many different ways; however, some important mechanisms of evolution are non-random. For example, consider the process of natural selection, which results in adaptations — features of organisms that appear to suit the environment in which the organisms live (e.g., the fit between a flower and its pollinator, the coordinated response of the immune system to pathogens, and the ability of bats to echolocate). Such amazing adaptations clearly did not come about “by chance.” They evolved via a combination of random and non-random processes. The process of mutation, which generates genetic variation, is random, but selection is non-random. Selection favored variants that were better able to survive and reproduce (e.g., to be pollinated, to fend off pathogens, or to navigate in the dark). Over many generations of random mutation and non-random selection, complex adaptations evolved. However, natural selection has no foresight and no intentions. Natural selection cannot select a trait that is unavailable in genetic variation. If a population or species doesn’t happen to have the right kinds of genetic variation, it will not evolve in response to the environmental changes and may become extinct. So although selection is not random, genetic variation is random, therefore chance or randomness is very significant factor in evolution of life.

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Scientists also have gained an understanding of the processes by which new species originate. A new species is one in which the individuals cannot mate and produce viable descendants with individuals of a preexisting species. The split of one species into two often starts because a group of individuals becomes geographically separated from the rest. This is particularly apparent in distant remote islands, such as the Galápagos and the Hawaiian archipelago, whose great distance from the Americas and Asia means that arriving colonizers will have little or no opportunity to mate with individuals remaining on those continents. Mountains, rivers, lakes, and other natural barriers also account for geographic separation between populations that once belonged to the same species. Once isolated, geographically separated groups of individuals become genetically differentiated as a consequence of mutation and other processes, including natural selection. The origin of a species is often a gradual process, so that at first the reproductive isolation between separated groups of organisms is only partial, but it eventually becomes complete. Scientists pay special attention to these intermediate situations, because they help to reconstruct the details of the process and to identify particular genes or sets of genes that account for the reproductive isolation between species. A particularly compelling example of speciation involves the 13 species of finches studied by Darwin on the Galápagos Islands, now known as Darwin’s finches. The ancestors of these finches appear to have immigrated from the South American mainland to the Galápagos. Today the different species of finches on the island have distinct habitats, diets, and behaviors, but the mechanisms involved in speciation continue to operate. A research group led by Peter and Rosemary Grant of Princeton University has shown that a single year of drought on the islands can drive evolutionary changes in the finches. Drought diminishes supplies of easily cracked nuts but permits the survival of plants that produce larger, tougher nuts. Droughts thus favor birds with strong, wide beaks that can break these tougher seeds, producing populations of birds with these traits. The Grants have estimated that if droughts occur about once every 10 years on the islands, a new species of finch might arise in only about 200 years.

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Human evolution is the evolutionary process that led to the emergence of anatomically modern humans, beginning with the evolutionary history of primates – in particular genus Homo – and leading to the emergence of Homo sapiens as a distinct species of the hominid family, the great apes. This process involved the gradual development of traits such as human bipedalism and language. The study of human evolution involves many scientific disciplines, including physical anthropology, primatology, archaeology, paleontology, neurobiology, ethology, linguistics, evolutionary psychology, embryology and genetics. Genetic studies show that primates diverged from other mammals about 85 million years ago, in the Late Cretaceous period, and the earliest fossils appear in the Paleocene, around 55 million years ago. Within the Hominoidea (apes) superfamily, the Hominidae family diverged from the Hylobatidae (gibbon) family some 15–20 million years ago; African great apes (subfamily Homininae) diverged from orangutans (Ponginae) about 14 million years ago; the Hominini tribe (humans, Australopithecines and other extinct biped genera, and chimpanzee) parted from the Gorillini tribe (gorillas) between 9 million years ago and 8 million years ago; and, in turn, the subtribes Hominina (humans and biped ancestors) and Panina (chimps) separated about 7.5 million years ago to 5.6 million years ago.

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A common misconception is that evolution has goals, long-term plans, or an innate tendency for “progress”, as expressed in beliefs such as orthogenesis and evolutionism; realistically however, evolution has no long-term goal and does not necessarily produce greater complexity. Although complex species have evolved, they occur as a side effect of the overall number of organisms increasing and simple forms of life still remain more common in the biosphere. For example, the overwhelming majority of species are microscopic prokaryotes, which form about half the world’s biomass despite their small size, and constitute the vast majority of Earth’s biodiversity. Simple organisms have therefore been the dominant form of life on Earth throughout its history and continue to be the main form of life up to the present day, with complex life only appearing more diverse because it is more noticeable. Indeed, the evolution of microorganisms is particularly important to modern evolutionary research, since their rapid reproduction allows the study of experimental evolution and the observation of evolution and adaptation in real time.

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Evolutionary history of life:

The evolutionary history of life on Earth traces the processes by which living and fossil organisms evolved since life appeared on the planet, until the present.

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Origin of life:

The Earth is about 4.54 billion years old. Highly energetic chemistry is thought to have produced a self-replicating molecule around 4 billion years ago, and half a billion years later the last common ancestor of all life existed. The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions. The beginning of life may have included self-replicating molecules such as RNA and the assembly of simple cells. All life on Earth shares a common ancestor known as the last universal common ancestor (LUCA), which lived approximately 3.5–3.8 billion years ago. A December 2017 report stated that 3.45 billion year old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth. Nonetheless, this should not be assumed to be the first living organism on Earth; a study in 2015 found “remains of biotic life” from 4.1 billion years ago in ancient rocks in Western Australia. In July 2016, scientists reported identifying a set of 355 genes from the LUCA of all organisms living on Earth. 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 Earth’s current species range from 10 million to 14 million, of which about 1.9 million are estimated to have been named and 1.6 million documented in a central database to date, leaving at least 80 percent not yet described. In May 2016, one study reported that 1 trillion species are estimated to be on Earth currently with only one-thousandth of one percent described. Another 2011 study predicts ∼8.7 million species globally, of which ∼2.2 million are marine. So even today we do not know total number of species on earth accurately.

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Evolution of life:

Prokaryotes inhabited the Earth from approximately 3–4 billion years ago. No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years. The eukaryotic cells emerged between 1.6–2.7 billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called endosymbiosis. The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or hydrogenosomes. Another engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants. The history of life was that of the unicellular eukaryotes, prokaryotes and archaea until about 610 million years ago when multicellular organisms began to appear in the oceans in the Ediacaran period. The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria. In January 2016, scientists reported that, about 800 million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells. Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over approximately 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis. About 500 million years ago, plants and fungi colonised the land and were soon followed by arthropods and other animals. Insects were particularly successful and even today make up the majority of animal species. Amphibians first appeared around 364 million years ago, followed by early amniotes and birds around 155 million years ago (both from “reptile”-like lineages), mammals around 129 million years ago, homininae around 10 million years ago and modern humans around 250,000 years ago. However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes.

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Life timeline:


Common descent:

All organisms on Earth are descended from a common ancestor or ancestral gene pool. Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events. The common descent of organisms was first deduced from four simple facts about organisms: First, they have geographic distributions that cannot be explained by local adaptation. Second, the diversity of life is not a set of completely unique organisms, but organisms that share morphological similarities. Third, vestigial traits with no clear purpose resemble functional ancestral traits and finally, that organisms can be classified using these similarities into a hierarchy of nested groups—similar to a family tree. However, modern research has suggested that, due to horizontal gene transfer, this “tree of life” may be more complicated than a simple branching tree since some genes have spread independently between distantly related species. Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry. More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and amino acids. The development of molecular genetics has revealed the record of evolution left in organisms’ genomes: dating when species diverged through the molecular clock produced by mutations. For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 96% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.

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Now I will discuss various processes related to evolution:

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Heredity:
Evolution in organisms occurs through changes in heritable traits—the inherited characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the “brown-eye trait” from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism’s genome (genetic material) is called its genotype. The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, many aspects of an organism’s phenotype are not inherited. For example, suntanned skin comes from the interaction between a person’s genotype and sunlight; thus, suntans are not passed on to people’s children. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn. Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long biopolymer composed of four types of bases. The sequences of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes). Recent findings have confirmed important examples of heritable changes that cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems. DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three-dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalisation. Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.

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Variation:
Individuals of a species have similar characteristics but they are rarely identical, the difference between them is called variation. Genetic variation is a result of subtle differences in our DNA. An individual organism’s phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation—when it either disappears from the population or replaces the ancestral allele entirely. Natural selection will only cause evolution if there is enough genetic variation in a population. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift. Variation comes from mutations in the genome, reshuffling of genes through sexual reproduction and migration between populations (gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species. However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.

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Genome variations in humans:

Genome variations are differences in the sequence of DNA from one person to the next. The more closely related two people are, the more similar their genomes. Scientists estimate that the genomes of non-related people—any two people plucked at random off the street—differ at about 1 in every 1,200 to 1,500 DNA bases, or “letters.” The haploid human genome contains approximately 3 billion base pairs of DNA packaged into 23 chromosomes. Of course, most cells in the body (except for female ova and male sperm) are diploid, with 23 pairs of chromosomes. That makes a total of 6 billion base pairs of DNA per cell. Each chromosome contains hundreds to thousands of genes, which carry the instructions for making proteins. Each of the estimated 30,000 genes in the human genome makes an average of three proteins. But we are all 99.9 percent the same, DNA-wise. (By contrast, we are only about 96 percent the same as our closest relatives, chimpanzees.). Variations are found all throughout the genome, on every one of the 46 human chromosomes. The majority of variations are found outside of genes, in the “extra” or “junk” DNA that does not affect a person’s characteristics. Mutations in these parts of the genome are never harmful, so variations can accumulate without causing any problems. Genes, by contrast, tend to be stable because mutations that occur in genes are often harmful to an individual, and thus less likely to be passed on. Genome variations include mutations and polymorphisms. Technically, a polymorphism is a DNA variation in which each possible sequence is present in at least 1 percent of people. For example, a place in the genome where 93 percent of people have a T and the remaining 7 percent have an A is a polymorphism. If one of the possible sequences is present in less than 1 percent of people (99.9 percent of people have a G and 0.1 percent have a C), then the variation is called a mutation. Informally, the term mutation is often used to refer to a harmful genome variation that is associated with a specific human disease, while the word polymorphism implies a variation that is neither harmful nor beneficial. However, scientists are now learning that many polymorphisms actually do affect a person’s characteristics, though in more complex and sometimes unexpected ways. About 90 percent of human genome variation comes in the form of single nucleotide polymorphisms, or SNPs (pronounced “snips”). As their name implies, these are variations that involve just one nucleotide, or base. Any one of the four DNA bases may be substituted for any other—an A instead of a T, a T instead of a C, a G instead of an A, and so on. Theoretically, a SNP could have four possible forms, or alleles, since there are four types of bases in DNA. But in reality, most SNPs have only two alleles. For example, if some people have a T at a certain place in their genome while everyone else has a G, that place in the genome is a SNP with a T allele and a G allele. The human genome contains more than 2 million SNPs.

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Genetic diversity vs. genetic variation:

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 variation is simply the variation in alleles of genes in the gene pool of a species or a population. Genetic variation lays the foundation for organisms to have genetic diversity, which contributes eventually for biodiversity through species diversity. Variety and variability collectively contribute for the diversity; hence, the existence of variations and diversity in genetic materials definitely helps the species to thrive through increased adaptability for the changing environmental conditions.



A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates. Traits that evolved through sexual selection are particularly prominent among males of several animal species. Although sexually favoured, traits such as cumbersome antlers, mating calls, large body size and bright colours often attract predation, which compromises the survival of individual males. This survival disadvantage is balanced by higher reproductive success in males that show these hard-to-fake, sexually selected traits.

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Natural selection most generally makes ‘nature’ the measure against which individuals and individual traits, are more or less likely to survive. “Nature” in this sense refers to an ecosystem, that is, a system in which organisms interact with every other element, physical as well as biological, in their local environment. Eugene Odum, a founder of ecology, defined an ecosystem as: “Any unit that includes all of the organisms…in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity and material cycles (i.e.: exchange of materials between living and nonliving parts) within the system.” Each population within an ecosystem occupies a distinct niche, or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the food chain and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection. Natural selection can act at different levels of organisation, such as genes, cells, individual organisms, groups of organisms and species. Selection can act at multiple levels simultaneously. An example of selection occurring below the level of the individual organism is genes called transposons, which can replicate and spread throughout a genome. Selection at a level above the individual, such as group selection, may allow the evolution of cooperation.

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Biased mutation:
In addition to being a major source of variation, mutation may also function as a mechanism of evolution when there are different probabilities at the molecular level for different mutations to occur, a process known as mutation bias. If two genotypes, for example one with the nucleotide G and another with the nucleotide A in the same position, have the same fitness, but mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes. Developmental or mutational biases have also been observed in morphological evolution. Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population. Mutations leading to the loss of function of a gene are much more common than mutations that produce a new, fully functional gene. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in Bacillus subtilis during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size, indicating that it is driven more by mutation bias than by genetic drift. In parasitic organisms, mutation bias leads to selection pressures as seen in Ehrlichia. Mutations are biased towards antigenic variants in outer-membrane proteins.

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Genetic drift:
Genetic drift is a change in the frequency of a population’s genes and alleles over time, often by founder effects (when a small group of individuals relocate) or bottlenecking (when a large population is decimated, leaving a smaller group to repopulate). That change occurs because alleles are subject to sampling error (i.e. random change). As a result, when selective forces are absent or relatively weak, allele frequencies tend to “drift” upward or downward randomly (in a random walk). This drift halts when an allele eventually becomes fixed, either by disappearing from the population, or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations with different sets of alleles. The time for a neutral allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations. It is usually difficult to measure the relative importance of selection and neutral processes, including genetic drift. The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of current research.

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Genetic hitchhiking:
Recombination allows alleles on the same strand of DNA to become separated. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other and genes that are close together tend to be inherited together, a phenomenon known as linkage. This tendency is measured by finding how often two alleles occur together on a single chromosome compared to expectations, which is called their linkage disequilibrium. A set of alleles that is usually inherited in a group is called a haplotype. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a selective sweep that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking or genetic draft. Genetic draft caused by the fact that some neutral genes are genetically linked to others that are under selection can be partially captured by an appropriate effective population size. Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain.

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Adaptation:
Adaptation is the process that makes organisms better suited to their habitat. Also, the term adaptation may refer to a trait that is important for an organism’s survival. For example, the adaptation of horses’ teeth to the grinding of grass. By using the term adaptation for the evolutionary process and adaptive trait for the product (the bodily part or function), the two senses of the word may be distinguished. Adaptations are produced by natural selection. Adaptation may cause either the gain of a new feature, or the loss of an ancestral feature. An example that shows both types of change is bacterial adaptation to antibiotic selection, with genetic changes causing antibiotic resistance by both modifying the target of the drug, or increasing the activity of transporters that pump the drug out of the cell.

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Adaptation occurs through the gradual modification of existing structures. Consequently, structures with similar internal organisation may have different functions in related organisms. This is the result of a single ancestral structure being adapted to function in different ways. The bones within bat wings, for example, are very similar to those in mice feet and primate hands, due to the descent of all these structures from a common mammalian ancestor. However, since all living organisms are related to some extent, even organs that appear to have little or no structural similarity, such as arthropod, squid and vertebrate eyes, or the limbs and wings of arthropods and vertebrates, can depend on a common set of homologous genes that control their assembly and function; this is called deep homology. During evolution, some structures may lose their original function and become vestigial structures. Such structures may have little or no function in a current species, yet have a clear function in ancestral species, or other closely related species. Examples include pseudogenes, the non-functional remains of eyes in blind cave-dwelling fish, wings in flightless birds, the presence of hip bones in whales and snakes, and sexual traits in organisms that reproduce via asexual reproduction. Examples of vestigial structures in humans include wisdom teeth, the coccyx, the vermiform appendix, and other behavioural vestiges such as goose bumps and primitive reflexes. However, many traits that appear to be simple adaptations are in fact exaptations: structures originally adapted for one function, but which coincidentally became somewhat useful for some other function in the process. One example is the African lizard Holaspis guentheri, which developed an extremely flat head for hiding in crevices, as can be seen by looking at its near relatives. However, in this species, the head has become so flattened that it assists in gliding from tree to tree—an exaptation. Within cells, molecular machines such as the bacterial flagella and protein sorting machinery evolved by the recruitment of several pre-existing proteins that previously had different functions. Another example is the recruitment of enzymes from glycolysis and xenobiotic metabolism to serve as structural proteins called crystallins within the lenses of organisms’ eyes.

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Adaptations can only occur if they are evolvable. Some adaptations which would prevent ill health are therefore not possible.

DNA cannot be totally prevented from undergoing somatic replication corruption; this has meant that cancer, which is caused by somatic mutations, has not (so far) been completely eliminated by natural selection.
Humans cannot biosynthesize vitamin C, and so risk scurvy, vitamin C deficiency disease, if dietary intake of the vitamin is insufficient.
Retinal neurons and their axon output have evolved to be inside the layer of retinal pigment cells. This creates a constraint on the evolution of the visual system such that the optic nerve is forced to exit the retina through a point called the optic disc. This, in turn, creates a blind spot. More importantly, it makes vision vulnerable to increased pressure within the eye (glaucoma) since this cups and damages the optic nerve at this point, resulting in impaired vision.
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Co-evolution:
Interactions between organisms can produce both conflict and cooperation. When the interaction is between pairs of species, such as a pathogen and a host, or a predator and its prey, these species can develop matched sets of adaptations. Here, the evolution of one species causes adaptations in a second species. These changes in the second species then, in turn, cause new adaptations in the first species. This cycle of selection and response is called coevolution. An example is the production of tetrodotoxin in the rough-skinned newt and the evolution of tetrodotoxin resistance in its predator, the common garter snake. In this predator-prey pair, an evolutionary arms race has produced high levels of toxin in the newt and correspondingly high levels of toxin resistance in the snake. Other examples of co-evolution that you need to know are: Hummingbirds and the flowers that they feed on have co-evolved. The flower is pollinated when the hummingbird drinks its nectar. The flower attracts the hummingbird whilst the bird’s beak is curved to allow it to reach the nectar; the caterpillar of the Old World Swallowtail butterfly has evolved to be resistant to the chemical defences of the fringed rue plant. This means that the caterpillar can feed on the plant without being poisoned.

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Cooperation:
Not all co-evolved interactions between species involve conflict. Many cases of mutually beneficial interactions have evolved. For instance, an extreme cooperation exists between plants and the mycorrhizal fungi that grow on their roots and aid the plant in absorbing nutrients from the soil. This is a reciprocal relationship as the plants provide the fungi with sugars from photosynthesis. Here, the fungi actually grow inside plant cells, allowing them to exchange nutrients with their hosts, while sending signals that suppress the plant immune system. Coalitions between organisms of the same species have also evolved. An extreme case is the eusociality found in social insects, such as bees, termites and ants, where sterile insects feed and guard the small number of organisms in a colony that are able to reproduce. On an even smaller scale, the somatic cells that make up the body of an animal limit their reproduction so they can maintain a stable organism, which then supports a small number of the animal’s germ cells to produce offspring. Here, somatic cells respond to specific signals that instruct them whether to grow, remain as they are, or die. If cells ignore these signals and multiply inappropriately, their uncontrolled growth causes cancer. Such cooperation within species may have evolved through the process of kin selection, which is where one organism acts to help raise a relative’s offspring. This activity is selected for because if the helping individual contains alleles which promote the helping activity, it is likely that its kin will also contain these alleles and thus those alleles will be passed on. Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.


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When humans faced extinction:

Humans may have come close to extinction about 70,000 years ago, according to the latest genetic research. The study suggests that at one point there may have been only 2,000 individuals alive as our species teetered on the brink. This means that, for a while, humanity was in a perilous state, vulnerable to disease, environmental disasters and conflict. If any of these factors had turned against us, we would not be here. The small genetic diversity of modern humans indicates that at some stage during the last 100,000 years, the human population dwindled to a very low level. It was out of this small population, with its consequent limited genetic diversity, that today’s humans descended.

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Neanderthals went Extinct:

Neanderthals emerged in Europe around 400,000 years ago. They began crossing paths 300,000 years later, as humans made their way into Neanderthal territory. Eventually, these encounters became more and more common and, for between 10,000 and 15,000 years, the two species co-existed and interbred—2 percent of our DNA comes from Neanderthals. Around 38,000 years ago, Neanderthals went extinct. Over recent decades two main theories of what caused their demise have emerged. The first is climate change—their decline coincides with a period of extreme cold in Western Europe that would have placed a huge amount of stress on the species. The other is competition with modern humans—our bigger brains and better adaptations to the environment at the time meant Neanderthals didn’t have a chance. The predominant theory is that early humans killed off the Neanderthal through competition for food and habitat. Homo sapiens’ superior brain power and hunting techniques meant the Neanderthals couldn’t compete. These two factors are not mutually exclusive and it is often suggested a combination of the two led to their downfall. Kolodny and Feldman’s new model says that irrespective of climate change and humans being at an evolutionary advantage, Neanderthals were always going to go extinct. Neanderthals did not go extinct because of climate change and competition with modern humans—they were doomed to be wiped out as a result of the evolutionary phenomenon of “random species drift.” As a result of “species drift,” humans slowly replaced Neanderthals until they dominated the landscape. This replacement, the researchers say, “was certain to occur, even in a selectively neutral setting, given the estimated migration pattern near the onset of the interaction between the two populations,” the researchers wrote.



The geologic time scale (GTS) is a system of chronological dating that relates geological strata (stratigraphy) to time. It is used by geologists, paleontologists, and other Earth scientists to describe the timing and relationships of events that have occurred during Earth’s history. The primary defined divisions of time are eons, in sequence the Hadean, the Archean, the Proterozoic and the Phanerozoic. The first three of these can be referred to collectively as the Precambrian supereon. Eons are divided into eras, which are in turn divided into periods, epochs and ages.