Meaning of the word evolution

In biology, evolution is the change in heritable characteristics of biological populations over successive generations.^[1][2] These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination.^[3] Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population.^[4] The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation.^[5][6]

The theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin’s book On the Origin of Species.^[7] Evolution by natural selection is established by observable facts about living organisms: (1) more offspring are often produced than can possibly survive; (2) traits vary among individuals with respect to their morphology, physiology, and behaviour (phenotypic variation); (3) different traits confer different rates of survival and reproduction (differential fitness); and (4) traits can be passed from generation to generation (heritability of fitness).^[8] In successive generations, members of a population are therefore more likely to be replaced by the offspring of parents with favourable characteristics. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis concluded Darwinian evolution acts on Mendelian genetic variation.^[9]

All life on Earth—including humanity—shares a last universal common ancestor (LUCA),^[10][11][12] which lived approximately 3.5–3.8 billion years ago.^[13] The fossil record includes a progression from early biogenic graphite^[14] to microbial mat fossils^[15][16][17] to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped by repeated formations of new species (speciation), changes within species (anagenesis), and loss of species (extinction) throughout the evolutionary history of life on Earth.^[18] Morphological and biochemical traits are more similar among species that share a more recent common ancestor, and these traits can be used to reconstruct phylogenetic trees.^[19][20]

Evolutionary biologists have continued to study various aspects of evolution by forming and testing hypotheses as well as constructing theories based on evidence from the field or laboratory and on data generated by the methods of mathematical and theoretical biology. Their discoveries have influenced not just the development of biology but numerous other scientific and industrial fields, including agriculture, medicine, and computer science.^[21]

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.^[22] Inherited traits are controlled by genes and the complete set of genes within an organism’s genome (genetic material) is called its genotype.^[23]

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.^[24] 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.^[25]

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information.^[23] DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specifies 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.^[26] 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).^[27][28]

Some heritable changes cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems.^[29] 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.^[30] 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.^[31] 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.^[32] Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.^[33][34]

Sources of variation

Evolution can occur if there is genetic variation within a population. 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.^[35] 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.^[36]

An individual organism’s phenotype results from both its genotype and the influence of the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation.^[28] 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.^[37]

Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variation would be rapidly lost, making evolution by natural selection implausible. 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.^[38]

Mutation

Mutations are changes in the DNA sequence of a cell’s genome and are the ultimate source of genetic variation in all organisms.^[3] When mutations occur, they may alter the product of a gene, or prevent the gene from functioning, or have no effect. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.^[39]

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome.^[40] Extra copies of genes are a major source of the raw material needed for new genes to evolve.^[41] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.^[42] For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.^[43]

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function.^[44][45] Other types of mutations can even generate entirely new genes from previously noncoding DNA, a phenomenon termed de novo gene birth.^[46][47]

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions (exon shuffling).^[48][49] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions.^[50] For example, polyketide synthases are large enzymes that make antibiotics; they contain up to 100 independent domains that each catalyse one step in the overall process, like a step in an assembly line.^[51]

One example of mutation is wild boar piglets. They are camouflage colored and show a characteristic pattern of dark and light longitudinal stripes. However, mutations in melanocortin 1 receptor (MC1R) disrupt the pattern. The majority of pig breeds carry MC1R mutations disrupting wild-type color and different mutations causing dominant black color of the pigs.^[52]

Sex and recombination

In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents’ chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes.^[53] Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles.^[54] Sex usually increases genetic variation and may increase the rate of evolution.^[55][56]

The two-fold cost of sex was first described by John Maynard Smith.^[57] The first cost is that in sexually dimorphic species only one of the two sexes can bear young. This cost does not apply to hermaphroditic species, like most plants and many invertebrates. The second cost is that any individual who reproduces sexually can only pass on 50% of its genes to any individual offspring, with even less passed on as each new generation passes.^[58] Yet sexual reproduction is the more common means of reproduction among eukaryotes and multicellular organisms. The Red Queen hypothesis has been used to explain the significance of sexual reproduction as a means to enable continual evolution and adaptation in response to coevolution with other species in an ever-changing environment.^{[58][59][60][61]} Another hypothesis is that sexual reproduction is primarily an adaptation for promoting accurate recombinational repair of damage in germline DNA, and that increased diversity is a byproduct of this process that may sometimes be adaptively beneficial.^[62][63]

Gene flow

Gene flow is the exchange of genes between populations and between species.^[64] It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy-metal-tolerant and heavy-metal-sensitive populations of grasses.

Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria.^[65] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species.^[66] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean weevil Callosobruchus chinensis has occurred.^[67][68] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi and plants.^[69] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.^[70]

Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.^[71]

Evolutionary processes

From a neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms,^[38] for example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, gene flow and mutation bias.

Natural selection

Evolution by natural selection is the process by which traits that enhance survival and reproduction become more common in successive generations of a population. It embodies three principles:^[8]

• Variation exists within populations of organisms with respect to morphology, physiology and behaviour (phenotypic variation).
• Different traits confer different rates of survival and reproduction (differential fitness).
• These traits can be passed from generation to generation (heritability of fitness).

More offspring are produced than can possibly survive, and these conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits to the next generation than those with traits that do not confer an advantage.^[72] 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.^[73] Consequences of selection include nonrandom mating^[74] and genetic hitchhiking.

The central concept of natural selection is the evolutionary fitness of an organism.^[75] Fitness is measured by an organism’s ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.^[75] However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism’s genes.^[76] For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.^[75]

If an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be «selected for.» Examples of traits that can increase fitness are enhanced survival and increased fecundity. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarer—they are «selected against.»^[77] Importantly, the fitness of an allele is not a fixed characteristic; if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful.^[26] However, even if the direction of selection does reverse in this way, traits that were lost in the past may not re-evolve in an identical form.^[78][79] However, a re-activation of dormant genes, as long as they have not been eliminated from the genome and were only suppressed perhaps for hundreds of generations, can lead to the re-occurrence of traits thought to be lost like hindlegs in dolphins, teeth in chickens, wings in wingless stick insects, tails and additional nipples in humans etc. «Throwbacks» such as these are known as atavisms.^[80]

Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is directional selection, which is a shift in the average value of a trait over time—for example, organisms slowly getting taller.^[81] Secondly, disruptive selection is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in stabilising selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity.^[72][82] This would, for example, cause organisms to eventually have a similar height.

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….»^[83] 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.^[84][85][86] Selection can act at multiple levels simultaneously.^[87] An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome.^[88] Selection at a level above the individual, such as group selection, may allow the evolution of cooperation.^[89]

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.^[90] 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.^[91] 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.^[92]

Sexual selection

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.^[94] 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.^[95][96] This survival disadvantage is balanced by higher reproductive success in males that show these hard-to-fake, sexually selected traits.^[97]

Genetic drift

Genetic drift is the random fluctuation of allele frequencies within a population from one generation to the next.^[98] When selective forces are absent or relatively weak, allele frequencies are equally likely to drift upward or downward^{[clarification needed]} in each successive generation because the alleles are subject to sampling error.^[99] This drift halts when an allele eventually becomes fixed, either by disappearing from the population or by 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 begin with the same genetic structure to drift apart into two divergent populations with different sets of alleles.^[100]

According to the now largely abandoned neutral theory of molecular evolution most evolutionary changes are the result of the fixation of neutral mutations by genetic drift.^[101] In this model, most genetic changes in a population are thus the result of constant mutation pressure and genetic drift.^[102] This form of the neutral theory is now largely abandoned since it does not seem to fit the genetic variation seen in nature.^[103][104] A better-supported version of this model is the nearly neutral theory, according to which a mutation that would be effectively neutral in a small population is not necessarily neutral in a large population.^[72] Other theories propose that genetic drift is dwarfed by other stochastic forces in evolution, such as genetic hitchhiking, also known as genetic draft.^{[99][92][105]} Another concept is constructive neutral evolution (CNE), which explains that complex systems can emerge and spread into a population through neutral transitions due to the principles of excess capacity, presuppression, and ratcheting,^{[106][107][108]} and it has been applied in areas ranging from the origins of the spliceosome to the complex interdependence of microbial communities.^{[109][110][111]}

The time it takes a neutral allele to become fixed by genetic drift depends on population size; fixation is more rapid in smaller populations.^[112] The number of individuals in a population is not critical, but instead a measure known as the effective population size.^[113] The effective population is usually smaller than the total population since it takes into account factors such as the level of inbreeding and the stage of the lifecycle in which the population is the smallest.^[113] The effective population size may not be the same for every gene in the same population.^[114]

It is usually difficult to measure the relative importance of selection and neutral processes, including drift.^[115] The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of current research.^[116]

Gene flow

Gene flow involves the exchange of genes between populations and between species.^[64] The presence or absence of gene flow fundamentally changes the course of evolution. Due to the complexity of organisms, any two completely isolated populations will eventually evolve genetic incompatibilities through neutral processes, as in the Bateson-Dobzhansky-Muller model, even if both populations remain essentially identical in terms of their adaptation to the environment.^{[citation needed]}

If genetic differentiation between populations develops, gene flow between populations can introduce traits or alleles which are disadvantageous in the local population and this may lead to organisms within these populations evolving mechanisms that prevent mating with genetically distant populations, eventually resulting in the appearance of new species. Thus, exchange of genetic information between individuals is fundamentally important for the development of the Biological Species Concept.^{[citation needed]}

During the development of the modern synthesis, Sewall Wright developed his shifting balance theory, which regarded gene flow between partially isolated populations as an important aspect of adaptive evolution.^[117] However, recently there has been substantial criticism of the importance of the shifting balance theory.^[118]

Mutation bias

Mutation bias is usually conceived as a difference in expected rates for two different kinds of mutation, e.g., transition-transversion bias, GC-AT bias, deletion-insertion bias. This is related to the idea of developmental bias. Haldane^[119] and Fisher^[120] argued that, because mutation is a weak pressure easily overcome by selection, tendencies of mutation would be ineffectual except under conditions of neutral evolution or extraordinarily high mutation rates. This opposing-pressures argument was long used to dismiss the possibility of internal tendencies in evolution,^[121] until the molecular era prompted renewed interest in neutral evolution.

Noboru Sueoka^[122] and Ernst Freese^[123] proposed that systematic biases in mutation might be responsible for systematic differences in genomic GC composition between species. The identification of a GC-biased E. coli mutator strain in 1967,^[124] along with the proposal of the neutral theory, established the plausibility of mutational explanations for molecular patterns, which are now common in the molecular evolution literature.

For instance, mutation biases are frequently invoked in models of codon usage.^[125] Such models also include effects of selection, following the mutation-selection-drift model,^[126] which allows both for mutation biases and differential selection based on effects on translation. Hypotheses of mutation bias have played an important role in the development of thinking about the evolution of genome composition, including isochores.^[127] Different insertion vs. deletion biases in different taxa can lead to the evolution of different genome sizes.^[128][129] The hypothesis of Lynch regarding genome size relies on mutational biases toward increase or decrease in genome size.

However, mutational hypotheses for the evolution of composition suffered a reduction in scope when it was discovered that (1) GC-biased gene conversion makes an important contribution to composition in diploid organisms such as mammals^[130] and (2) bacterial genomes frequently have AT-biased mutation.^[131]

Contemporary thinking about the role of mutation biases reflects a different theory from that of Haldane and Fisher. More recent work^[121] showed that the original «pressures» theory assumes that evolution is based on standing variation: when evolution depends on events of mutation that introduce new alleles, mutational and developmental biases in the introduction of variation can impose biases on evolution without requiring neutral evolution or high mutation rates (^[121]; see also ^[132]).

Several studies report that the mutations implicated in adaptation reflect common mutation biases^{[133][134][135]} though others dispute this interpretation.^[136]

Applications

Concepts and models used in evolutionary biology, such as natural selection, have many applications.^[137]

Artificial selection is the intentional selection of traits in a population of organisms. This has been used for thousands of years in the domestication of plants and animals.^[138] 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. Proteins with valuable properties have evolved by repeated rounds of mutation and selection (for example modified enzymes and new antibodies) in a process called directed evolution.^[139]

Understanding the changes that have occurred during an organism’s evolution can reveal the genes needed to construct parts of the body, genes which may be involved in human genetic disorders.^[140] For example, the Mexican tetra is an albino cavefish that lost its eyesight during evolution. Breeding together different populations of this blind fish produced some offspring with functional eyes, since different mutations had occurred in the isolated populations that had evolved in different caves.^[141] This helped identify genes required for vision and pigmentation.^[142]

Evolutionary theory has many applications in medicine. Many human diseases are not static phenomena, but capable of evolution. Viruses, bacteria, fungi and cancers evolve to be resistant to host immune defences, as well as to pharmaceutical drugs.^{[143][144][145]} These same problems occur in agriculture with pesticide^[146] and herbicide^[147] resistance. It is possible that we are facing the end of the effective life of most of available antibiotics^[148] and predicting the evolution and evolvability^[149] of our pathogens and devising strategies to slow or circumvent it is requiring deeper knowledge of the complex forces driving evolution at the molecular level.^[150]

In computer science, simulations of evolution using evolutionary algorithms and artificial life started in the 1960s and were extended with simulation of artificial selection.^[151] Artificial evolution became a widely recognised optimisation method as a result of the work of Ingo Rechenberg in the 1960s. He used evolution strategies to solve complex engineering problems.^[152] Genetic algorithms in particular became popular through the writing of John Henry Holland.^[153] Practical applications also include automatic evolution of computer programmes.^[154] Evolutionary algorithms are now used to solve multi-dimensional problems more efficiently than software produced by human designers and also to optimise the design of systems.^[155]

Natural outcomes

Evolution influences every aspect of the form and behaviour of organisms. Most prominent are the specific behavioural and physical adaptations that are the outcome of natural selection. These adaptations increase fitness by aiding activities such as finding food, avoiding predators or attracting mates. Organisms can also respond to selection by cooperating with each other, usually by aiding their relatives or engaging in mutually beneficial symbiosis. In the longer term, evolution produces new species through splitting ancestral populations of organisms into new groups that cannot or will not interbreed. These outcomes of evolution are distinguished based on time scale as macroevolution versus microevolution. Macroevolution refers to evolution that occurs at or above the level of species, in particular speciation and extinction; whereas microevolution refers to smaller evolutionary changes within a species or population, in particular shifts in allele frequency and adaptation.^[157] Macroevolution the outcome of long periods of microevolution.^[158] Thus, the distinction between micro- and macroevolution is not a fundamental one—the difference is simply the time involved.^[159] However, in macroevolution, the traits of the entire species may be important. For instance, a large amount of variation among individuals allows a species to rapidly adapt to new habitats, lessening the chance of it going extinct, while a wide geographic range increases the chance of speciation, by making it more likely that part of the population will become isolated. In this sense, microevolution and macroevolution might involve selection at different levels—with microevolution acting on genes and organisms, versus macroevolutionary processes such as species selection acting on entire species and affecting their rates of speciation and extinction.^{[160][161][162]}

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.^{[163][164][165]} 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.^[166] For example, the overwhelming majority of species are microscopic prokaryotes, which form about half the world’s biomass despite their small size,^[167] and constitute the vast majority of Earth’s biodiversity.^[168] 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.^[169] Indeed, the evolution of microorganisms is particularly important to evolutionary research, since their rapid reproduction allows the study of experimental evolution and the observation of evolution and adaptation in real time.^[170][171]

Adaptation

Adaptation is the process that makes organisms better suited to their habitat.^[172][173] 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.^[174] The following definitions are due to Theodosius Dobzhansky:

1. Adaptation is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.^[175]
2. Adaptedness is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.^[176]
3. 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.^[177]

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.^[178] Other striking examples are the bacteria Escherichia coli evolving the ability to use citric acid as a nutrient in a long-term laboratory experiment,^[179] Flavobacterium evolving a novel enzyme that allows these bacteria to grow on the by-products of nylon manufacturing,^[180][181] and the soil bacterium Sphingobium evolving an entirely new metabolic pathway that degrades the synthetic pesticide pentachlorophenol.^[182][183] An interesting but still controversial idea is that some adaptations might increase the ability of organisms to generate genetic diversity and adapt by natural selection (increasing organisms’ evolvability).^{[184][185][186][187]}

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.^[189] However, since all living organisms are related to some extent,^[190] 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.^[191][192]

During evolution, some structures may lose their original function and become vestigial structures.^[193] 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,^[194] the non-functional remains of eyes in blind cave-dwelling fish,^[195] wings in flightless birds,^[196] the presence of hip bones in whales and snakes,^[188] and sexual traits in organisms that reproduce via asexual reproduction.^[197] Examples of vestigial structures in humans include wisdom teeth,^[198] the coccyx,^[193] the vermiform appendix,^[193] and other behavioural vestiges such as goose bumps^[199][200] and primitive reflexes.^{[201][202][203]}

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.^[204] 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.^[204] Within cells, molecular machines such as the bacterial flagella^[205] and protein sorting machinery^[206] evolved by the recruitment of several pre-existing proteins that previously had different functions.^[157] 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.^[207][208]

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations and exaptations.^[209] This research addresses the origin and evolution of embryonic development and how modifications of development and developmental processes produce novel features.^[210] These studies have shown that evolution can alter development to produce new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the middle ear in mammals.^[211] It is also possible for structures that have been lost in evolution to reappear due to changes in developmental genes, such as a mutation in chickens causing embryos to grow teeth similar to those of crocodiles.^[212] It is now becoming clear that most alterations in the form of organisms are due to changes in a small set of conserved genes.^[213]

Coevolution

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.^[214] 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.^[215]

Cooperation

Not all co-evolved interactions between species involve conflict.^[216] 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.^[217] 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.^[218]

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.^[219]

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.^[220] 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.^[221] Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.^[222]

Speciation

Speciation is the process where a species diverges into two or more descendant species.^[223]

There are multiple ways to define the concept of «species.» The choice of definition is dependent on the particularities of the species concerned.^[224] For example, some species concepts apply more readily toward sexually reproducing organisms while others lend themselves better toward asexual organisms. Despite the diversity of various species concepts, these various concepts can be placed into one of three broad philosophical approaches: interbreeding, ecological and phylogenetic.^[225] The Biological Species Concept (BSC) is a classic example of the interbreeding approach. Defined by evolutionary biologist Ernst Mayr in 1942, the BSC states that «species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups.»^[226] Despite its wide and long-term use, the BSC like others is not without controversy, for example because these concepts cannot be applied to prokaryotes;^[227] this is called the species problem.^[224] Some researchers have attempted a unifying monistic definition of species, while others adopt a pluralistic approach and suggest that there may be different ways to logically interpret the definition of a species.^[224][225]

Barriers to reproduction between two diverging sexual populations are required for the populations to become new species. Gene flow may slow this process by spreading the new genetic variants also to the other populations. Depending on how far two species have diverged since their most recent common ancestor, it may still be possible for them to produce offspring, as with horses and donkeys mating to produce mules.^[228] Such hybrids are generally infertile. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype.^[229] The importance of hybridisation in producing new species of animals is unclear, although cases have been seen in many types of animals,^[230] with the gray tree frog being a particularly well-studied example.^[231]

Speciation has been observed multiple times under both controlled laboratory conditions and in nature.^[232] In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four primary geographic modes of speciation. The most common in animals is allopatric speciation, which occurs in populations initially isolated geographically, such as by habitat fragmentation or migration. Selection under these conditions can produce very rapid changes in the appearance and behaviour of organisms.^[233][234] As selection and drift act independently on populations isolated from the rest of their species, separation may eventually produce organisms that cannot interbreed.^[235]

The second mode of speciation is peripatric speciation, which occurs when small populations of organisms become isolated in a new environment. This differs from allopatric speciation in that the isolated populations are numerically much smaller than the parental population. Here, the founder effect causes rapid speciation after an increase in inbreeding increases selection on homozygotes, leading to rapid genetic change.^[236]

The third mode is parapatric speciation. This is similar to peripatric speciation in that a small population enters a new habitat, but differs in that there is no physical separation between these two populations. Instead, speciation results from the evolution of mechanisms that reduce gene flow between the two populations.^[223] Generally this occurs when there has been a drastic change in the environment within the parental species’ habitat. One example is the grass Anthoxanthum odoratum, which can undergo parapatric speciation in response to localised metal pollution from mines.^[237] Here, plants evolve that have resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produced a gradual change in the flowering time of the metal-resistant plants, which eventually produced complete reproductive isolation. Selection against hybrids between the two populations may cause reinforcement, which is the evolution of traits that promote mating within a species, as well as character displacement, which is when two species become more distinct in appearance.^[238]

Finally, in sympatric speciation species diverge without geographic isolation or changes in habitat. This form is rare since even a small amount of gene flow may remove genetic differences between parts of a population.^[239] Generally, sympatric speciation in animals requires the evolution of both genetic differences and nonrandom mating, to allow reproductive isolation to evolve.^[240]

One type of sympatric speciation involves crossbreeding of two related species to produce a new hybrid species. This is not common in animals as animal hybrids are usually sterile. This is because during meiosis the homologous chromosomes from each parent are from different species and cannot successfully pair. However, it is more common in plants because plants often double their number of chromosomes, to form polyploids.^[241] This allows the chromosomes from each parental species to form matching pairs during meiosis, since each parent’s chromosomes are represented by a pair already.^[242] An example of such a speciation event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa crossbred to give the new species Arabidopsis suecica.^[243] This happened about 20,000 years ago,^[244] and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process.^[245] Indeed, chromosome doubling within a species may be a common cause of reproductive isolation, as half the doubled chromosomes will be unmatched when breeding with undoubled organisms.^[246]

Speciation events are important in the theory of punctuated equilibrium, which accounts for the pattern in the fossil record of short «bursts» of evolution interspersed with relatively long periods of stasis, where species remain relatively unchanged.^[247] In this theory, speciation and rapid evolution are linked, with natural selection and genetic drift acting most strongly on organisms undergoing speciation in novel habitats or small populations. As a result, the periods of stasis in the fossil record correspond to the parental population and the organisms undergoing speciation and rapid evolution are found in small populations or geographically restricted habitats and therefore rarely being preserved as fossils.^[161]

Extinction

Extinction is the disappearance of an entire species. Extinction is not an unusual event, as species regularly appear through speciation and disappear through extinction.^[248] Nearly all animal and plant species that have lived on Earth are now extinct,^[249] and extinction appears to be the ultimate fate of all species.^[250] These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events.^[251] The Cretaceous–Paleogene extinction event, during which the non-avian dinosaurs became extinct, is the most well-known, but the earlier Permian–Triassic extinction event was even more severe, with approximately 96% of all marine species driven to extinction.^[251] The Holocene extinction event is an ongoing mass extinction associated with humanity’s expansion across the globe over the past few thousand years. Present-day extinction rates are 100–1000 times greater than the background rate and up to 30% of current species may be extinct by the mid 21st century.^[252] Human activities are now the primary cause of the ongoing extinction event;^[253][254] global warming may further accelerate it in the future.^[255] Despite the estimated extinction of more than 99% of all species that ever lived on Earth,^[256][257] about 1 trillion species are estimated to be on Earth currently with only one-thousandth of 1% described.^[258]

The role of extinction in evolution is not very well understood and may depend on which type of extinction is considered.^[251] The causes of the continuous «low-level» extinction events, which form the majority of extinctions, may be the result of competition between species for limited resources (the competitive exclusion principle).^[259] If one species can out-compete another, this could produce species selection, with the fitter species surviving and the other species being driven to extinction.^[85] The intermittent mass extinctions are also important, but instead of acting as a selective force, they drastically reduce diversity in a nonspecific manner and promote bursts of rapid evolution and speciation in survivors.^[260]

Evolutionary history of life

Origin of life

The Earth is about 4.54 billion years old.^{[261][262][263]} The earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago,^[13][264] during the Eoarchean Era after a geological crust started to solidify following the earlier molten Hadean Eon. Microbial mat fossils have been found in 3.48 billion-year-old sandstone in Western Australia.^[15][16][17] Other early physical evidence of a biogenic substance is graphite in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland^[14] as well as «remains of biotic life» found in 4.1 billion-year-old rocks in Western Australia.^[265][266] Commenting on the Australian findings, Stephen Blair Hedges wrote, «If life arose relatively quickly on Earth, then it could be common in the universe.»^[265][267] In July 2016, scientists reported identifying a set of 355 genes from the last universal common ancestor (LUCA) of all organisms living on Earth.^[268]

More than 99% of all species, amounting to over five billion species,^[269] that ever lived on Earth are estimated to be extinct.^[256][257] Estimates on the number of Earth’s current species range from 10 million to 14 million,^[270][271] of which about 1.9 million are estimated to have been named^[272] and 1.6 million documented in a central database to date,^[273] leaving at least 80% not yet described.

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.^[11] The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions.^[274][275] The beginning of life may have included self-replicating molecules such as RNA^[276] and the assembly of simple cells.^[277]

Common descent

All organisms on Earth are descended from a common ancestor or ancestral gene pool.^[190][278] Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events.^[279] 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. Fourth, organisms can be classified using these similarities into a hierarchy of nested groups, similar to a family tree.^[280]

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.^[281][282] To solve this problem and others, some authors prefer to use the «Coral of life» as a metaphor or a mathematical model to illustrate the evolution of life. This view dates back to an idea briefly mentioned by Darwin but later abandoned.^[283]

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.^[284] By comparing the anatomies of both modern and extinct species, palaeontologists 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.^[285] 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.^[286] For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.^[287]

Evolution of life

Prokaryotes inhabited the Earth from approximately 3–4 billion years ago.^[289][290] No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years.^[291] The eukaryotic cells emerged between 1.6 and 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.^[292][293] The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or hydrogenosomes.^[294] Another engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.^[295]

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.^[289][296] The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria.^[297] 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.^[298]

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.^[299] Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.^[300]

About 500 million years ago, plants and fungi colonised the land and were soon followed by arthropods and other animals.^[301] Insects were particularly successful and even today make up the majority of animal species.^[302] 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.^{[303][304][305]} 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.^[168]

History of evolutionary thought

Classical antiquity

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 and Empedocles.^[307] Such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura (On the Nature of Things).^[308][309]

Middle Ages

In contrast to these materialistic views, Aristotelianism had considered all natural things as actualisations of fixed natural possibilities, known as forms.^[310][311] This became part of a medieval teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages and were integrated into Christian learning, but Aristotle did not demand that real types of organisms always correspond one-for-one with exact metaphysical forms and specifically gave examples of how new types of living things could come to be.^[312]

A number of Arab Muslim scholars wrote about evolution, most notably Ibn Khaldun, who wrote the book Muqaddimah in 1377 AD, in which he asserted that humans developed from «the world of the monkeys», in a process by which «species become more numerous».^[313]

Pre-Darwinian

The «New Science» of the 17th century rejected the Aristotelian approach. It sought to explain natural phenomena in terms of physical laws that were the same for all visible things and that did not require the existence of any fixed natural categories or divine cosmic order. However, this new approach was slow to take root in the biological sciences: the last bastion of the concept of fixed natural types. John Ray applied one of the previously more general terms for fixed natural types, «species», to plant and animal types, but he strictly identified each type of living thing as a species and proposed that each species could be defined by the features that perpetuated themselves generation after generation.^[314] The biological classification introduced by Carl Linnaeus in 1735 explicitly recognised the hierarchical nature of species relationships, but still viewed species as fixed according to a divine plan.^[315]

Other naturalists of this time speculated on the evolutionary change of species over time according to natural laws. In 1751, Pierre Louis Maupertuis wrote of natural modifications occurring during reproduction and accumulating over many generations to produce new species.^[316] Georges-Louis Leclerc, Comte de Buffon, suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single microorganism (or «filament»).^[317] The first full-fledged evolutionary scheme was Jean-Baptiste Lamarck’s «transmutation» theory of 1809,^[318] which envisaged spontaneous generation continually producing simple forms of life that developed greater complexity in parallel lineages with an inherent progressive tendency, and postulated that on a local level, these lineages adapted to the environment by inheriting changes caused by their use or disuse in parents.^[319] (The latter process was later called Lamarckism.)^{[319][320][321]} These ideas were condemned by established naturalists as speculation lacking empirical support. In particular, Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray’s ideas of benevolent design had been developed by William Paley into the Natural Theology or Evidences of the Existence and Attributes of the Deity (1802), which proposed complex adaptations as evidence of divine design and which was admired by Charles Darwin.^[322][323]

Darwinian revolution

The crucial break from the concept of constant typological classes or types in biology came with the theory of evolution through natural selection, which was formulated by Charles Darwin and Alfred Wallace in terms of variable populations. Darwin used the expression «descent with modification» rather than «evolution».^[324] Partly influenced by An Essay on the Principle of Population (1798) by Thomas Robert Malthus, Darwin noted that population growth would lead to a «struggle for existence» in which favourable variations prevailed as others perished. In each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of plants and animals from a common ancestry through the working of natural laws in the same way for all types of organism.^{[325][326][327][328]} Darwin developed his theory of «natural selection» from 1838 onwards and was writing up his «big book» on the subject when Alfred Russel Wallace sent him a version of virtually the same theory in 1858. Their separate papers were presented together at an 1858 meeting of the Linnean Society of London.^[329] At the end of 1859, Darwin’s publication of his «abstract» as On the Origin of Species explained natural selection in detail and in a way that led to an increasingly wide acceptance of Darwin’s concepts of evolution at the expense of alternative theories. Thomas Henry Huxley applied Darwin’s ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.^[330]

Pangenesis and heredity

The mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis.^[331] In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel’s laws of inheritance eventually supplanted most of Darwin’s pangenesis theory.^[332] August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin’s pangenesis theory to Weismann’s germ/soma cell distinction and proposed that Darwin’s pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cell’s structure. De Vries was also one of the researchers who made Mendel’s work well known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.^[333] To explain how new variants originate, de Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.^[334][335] In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin’s theory, genetic mutations, and Mendelian inheritance was thus reconciled.^[336]

The ‘modern synthesis’

In the 1920s and 1930s, the so-called modern synthesis connected natural selection and population genetics, based on Mendelian inheritance, into a unified theory that applied generally to any branch of biology. It explained patterns observed across species in populations, through fossil transitions in palaeontology.^[336]

Further syntheses

Since then, further syntheses have extended evolution’s explanatory power in the light of numerous discoveries, to cover biological phenomena across the whole of the biological hierarchy from genes to populations.^[337]

The publication of the structure of DNA by James Watson and Francis Crick with contribution of Rosalind Franklin in 1953 demonstrated a physical mechanism for inheritance.^[338] Molecular biology improved understanding of the relationship between genotype and phenotype. Advances were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees.^[339] In 1973, evolutionary biologist Theodosius Dobzhansky penned that «nothing in biology makes sense except in the light of evolution,» because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.^[340]

One extension, known as evolutionary developmental biology and informally called «evo-devo,» emphasises how changes between generations (evolution) act on patterns of change within individual organisms (development).^[259][341] Since the beginning of the 21st century, some biologists have argued for an extended evolutionary synthesis, which would account for the effects of non-genetic inheritance modes, such as epigenetics, parental effects, ecological inheritance and cultural inheritance, and evolvability.^[342][343]

Social and cultural responses

In the 19th century, particularly after the publication of On the Origin of Species in 1859, the idea that life had evolved was an active source of academic debate centred on the philosophical, social and religious implications of evolution. Today, the modern evolutionary synthesis is accepted by a vast majority of scientists.^[259] However, evolution remains a contentious concept for some theists.^[345]

While various religions and denominations have reconciled their beliefs with evolution through concepts such as theistic evolution, there are creationists who believe that evolution is contradicted by the creation myths found in their religions and who raise various objections to evolution.^{[157][346][347]} As had been demonstrated by responses to the publication of Vestiges of the Natural History of Creation in 1844, the most controversial aspect of evolutionary biology is the implication of human evolution that humans share common ancestry with apes and that the mental and moral faculties of humanity have the same types of natural causes as other inherited traits in animals.^[348] In some countries, notably the United States, these tensions between science and religion have fuelled the current creation–evolution controversy, a religious conflict focusing on politics and public education.^[349] While other scientific fields such as cosmology^[350] and Earth science^[351] also conflict with literal interpretations of many religious texts, evolutionary biology experiences significantly more opposition from religious literalists.

The teaching of evolution in American secondary school biology classes was uncommon in most of the first half of the 20th century. The Scopes Trial decision of 1925 caused the subject to become very rare in American secondary biology textbooks for a generation, but it was gradually re-introduced later and became legally protected with the 1968 Epperson v. Arkansas decision. Since then, the competing religious belief of creationism was legally disallowed in secondary school curricula in various decisions in the 1970s and 1980s, but it returned in pseudoscientific form as intelligent design (ID), to be excluded once again in the 2005 Kitzmiller v. Dover Area School District case.^[352] The debate over Darwin’s ideas did not generate significant controversy in China.^[353]

References

Bibliography

Further reading

External links

General information

• «Evolution» on In Our Time at the BBC
• «Evolution Resources from the National Academies». Washington, DC: National Academy of Sciences. Retrieved 30 May 2011.
• «Understanding Evolution: your one-stop resource for information on evolution». Berkeley, California: University of California, Berkeley. Retrieved 30 May 2011.
• «Evolution of Evolution – 150 Years of Darwin’s ‘On the Origin of Species’«. Arlington County, Virginia: National Science Foundation. Archived from the original on 19 May 2011. Retrieved 30 May 2011.
• «Human Evolution Timeline Interactive». Smithsonian Institution, National Museum of Natural History. 28 January 2010. Retrieved 14 July 2018. Adobe Flash required.
• «History of Evolution in the United States». Salon (Retrieved 2021-08-24)
• Video (1980; Cosmos animation; 8:01): «Evolution» – Carl Sagan on YouTube

Experiments

• Lenski, Richard E. «Experimental Evolution». East Lansing, Michigan: Michigan State University. Retrieved 31 July 2013.
• Chastain, Erick; Livnat, Adi; Papadimitriou, Christos; Vazirani, Umesh (22 July 2014). «Algorithms, games, and evolution». PNAS. 111 (29): 10620–10623. Bibcode:2014PNAS..11110620C. doi:10.1073/pnas.1406556111. ISSN 0027-8424. PMC 4115542. PMID 24979793.

Online lectures

• «Evolution Matters Lecture Series». Harvard Online Learning Portal. Cambridge, Massachusetts: Harvard University. Archived from the original on 18 December 2017. Retrieved 15 July 2018.
• Stearns, Stephen C. «EEB 122: Principles of Evolution, Ecology and Behavior». Open Yale Courses. New Haven, Connecticut: Yale University. Archived from the original on 1 December 2017. Retrieved 14 July 2018.

Evolution is a biological process. It is how living things change over time and how new species develop. The theory of evolution explains how evolution works, and how living and extinct things have come to be the way they are.^[1] The theory of evolution is a very important idea in biology. Theodosius Dobzhansky, a well-known evolutionary biologist, said: «Nothing in biology makes sense except in the light of evolution».^[2]

Evolution has been happening since life started on Earth and is happening now. Evolution is caused mostly by natural selection. Living things are not identical to each other. Even living things of the same species look, move, and behave differently to some extent. Some differences make it easier for living things to survive and reproduce. Differences may make it easier to find food, hide from danger, or give birth to offspring which survive. The offspring have some of the things which made it easier for their parents to have them. Over time, these differences continue, and living things change enough to become new species.

It is known that living things have changed over time, because their remains can be seen in the rocks. These remains are called ‘fossils’. This proves that the animals and plants of today are different from those of long ago. The older the fossils, the bigger the differences from modern forms.^[3] This has happened because evolution has taken place. That evolution has taken place is a fact, because it is overwhelmingly supported by many lines of evidence.^[4][5][6] At the same time, evolutionary questions are still being actively researched by biologists.

Comparison of DNA sequences allows organisms to be grouped by how similar their sequences are. In 2010 an analysis compared sequences to phylogenetic trees, and supported the idea of common descent. There is now «strong quantitative support, by a formal test»,^[7] for the unity of life.^[8]

Evidence[change | change source]

The evidence for evolution is given in a number of books.^{[9][10][11][12]} Some of this evidence is discussed here.

Fossils show that change has occurred[change | change source]

The realization that some rocks contain fossils was a very important event in natural history. There are three parts to this story:

1. The realization that things in rocks which looked organic actually were the altered remains of living things. This was settled in the 16th and 17th centuries by Conrad Gessner, Nicolaus Steno, Robert Hooke and others.^[13][14]

2. The realization that many fossils represented species which do not exist today. It was Georges Cuvier, the comparative anatomist, who proved that extinction occurred and that different strata contained different fossils.^[15]p108

3. The realization that early fossils were simpler organisms than later fossils. Also, the later the rocks, the more like the present day are the fossils.^[16]

«The most convincing evidence for the occurrence of evolution is the discovery of extinct organisms in older geological strata… The older the strata are…the more different the fossil will be from living representatives… that is to be expected if the fauna and flora of the earlier strata had gradually evolved into their descendants. Ernst Mayr ^[1]p13

Geographical distribution[change | change source]

Where species live is a topic which fascinated both Charles Darwin and Alfred Russel Wallace.^[17][18][19] When new species occur, usually by the splitting of older species, this takes place in one place in the world. Once it is established, a new species may spread to some places and not others.

Australasia[change | change source]

Australasia has been separated from other continents for many millions of years. In the main part of the continent, Australia, 83% of mammals, 89% of reptiles, 90% of fish and insects, and 93% of amphibians are endemic.^[20] Its native mammals are mostly marsupials like kangaroos, bandicoots, and quolls.^[21] By contrast, marsupials are today totally absent from Africa and form a small portion of the mammalian fauna of South America, where opossums, shrew opossums, and the monito del monte occur (see the Great American Interchange).

The only living representatives of primitive egg-laying mammals (monotremes) are the echidnas and the platypus. They are only found in Australasia, which includes Tasmania, New Guinea, and Kangaroo Island. These monotremes are totally absent in the rest of the world.^[22] On the other hand, Australia is missing many groups of placental mammals that are common on other continents (carnivora, artiodactyls, shrews, squirrels, lagomorphs), although it does have indigenous bats and rodents, which arrived later.^[23]

The evolutionary story is that placental mammals evolved in Eurasia, and wiped out the marsupials and monotremes wherever they spread. They did not reach Australasia until more recently. That is the simple reason why Australia has most of the world’s marsupials and all the world’s monotremes.

Evolution of horses[change | change source]

The evolution of the horse family (Equidae) is a good example of the way that evolution works. The oldest fossil of a horse is about 52 million years old. It was a small animal with five toes on the front feet and four on the hind feet. At that time, there were more forests in the world than today. This horse lived in woodland, eating leaves, nuts and fruit with its simple teeth. It was only about as big as a fox.^[24]

About 30 million years ago the world started to become cooler and drier. Forests shrank; grassland expanded, and horses changed. They ate grass, they grew larger, and they ran faster because they had to escape faster predators. Because grass wears teeth out, horses with longer-lasting teeth had an advantage.

For most of this long period of time, there were a number of horse types (genera). Now only one genus exists: the modern horse, Equus. It has teeth which grow all its life, hooves on single toes, great long legs for running, and the animal is big and strong enough to survive in the open plain.^[24] Horses lived in western Canada until 12,000 years ago,^[25] but all horses in North America became extinct about 11,000 years ago. The causes of this extinction are not yet clear. Climate change and over-hunting by humans are suggested.

So, scientists can see that changes have happened. They have happened slowly over a long time. How these changes have come about is explained by the theory of evolution.

Hawaiian Drosophila (fruit flies)[change | change source]

In about 6,500 sq mi (17,000 km²), the Hawaiian Islands have the most diverse collection of Drosophila flies in the world, living from rainforests to mountain meadows. About 800 Hawaiian fruit fly species are known.

Genetic evidence shows that all the native fruit fly species in Hawaiʻi have descended from a single ancestral species that came to the islands, about 20 million years ago. Later adaptive radiation was caused by a lack of competition and a wide variety of vacant niches. Although it would be possible for a single pregnant female to colonise an island, it is more likely to have been a group from the same species.^{[26][27][28][29]}

Distribution of Glossopteris[change | change source]

The combination of continental drift and evolution can explain what is found in the fossil record. Glossopteris is an extinct species of seed fern plants from the Permian period on the ancient supercontinent of Gondwana.^[30]

Glossopteris fossils are found in Permian strata in southeast South America, southeast Africa, all of Madagascar, northern India, all of Australia, all of New Zealand, and scattered on the southern and northern edges of Antarctica.

During the Permian, these continents were connected as Gondwana. This is known from magnetic striping in the rocks, other fossil distributions, and glacial scratches pointing away from the temperate climate of the South Pole during the Permian.^[11]p103

Common descent[change | change source]

When biologists look at living things, they see that animals and plants belong to groups which have something in common. Charles Darwin explained that this followed naturally if «we admit the common parentage of allied forms, together with their modification through variation and natural selection».^{[17]p402[9]p456}

For example, all insects are related. They share a basic body plan, whose development is controlled by master regulatory genes.^[31] They have six legs; they have hard parts on the outside of the body (an exoskeleton); they have eyes formed of many separate chambers, and so on. Biologists explain this with evolution. All insects are the descendants of a group of animals who lived a long time ago. They still keep the basic plan (six legs and so on) but the details change. They look different now because they changed in different ways: this is evolution.^[32]

It was Darwin who first suggested that all life on Earth had a single origin, and from that beginning «endless forms most beautiful and most wonderful have been, and are being, evolved».^[9]p490[17] Evidence from molecular biology in recent years has supported the idea that all life is related by common descent.^[33]

Vestigial structures[change | change source]

Strong evidence for common descent comes from vestigial structures.^[17]p397 The useless wings of flightless beetles are sealed under fused wing covers. This can be simply explained by their descent from ancestral beetles which had wings that worked.^[12]p49

Rudimentary body parts, those that are smaller and simpler in structure than corresponding parts in ancestral species, are called vestigial organs. Those organs are functional in the ancestral species but are now either nonfunctional or re-adapted to a new function. Examples are the pelvic girdles of whales, halteres (hind wings) of flies, wings of flightless birds, and the leaves of some xerophytes (e.g. cactus) and parasitic plants (e.g. dodder).

However, vestigial structures may have their original function replaced with another. For example, the halteres in flies help balance the insect while in flight, and the wings of ostriches are used in mating rituals and aggressive displays. The ear ossicles in mammals are former bones of the lower jaw.

«Rudimentary organs plainly declare their origin and meaning…» (p262). «Rudimentary organs… are the record of a former state of things, and have been retained solely through the powers of inheritance… far from being a difficulty, as they assuredly do on the old doctrine of creation, might even have been anticipated in accordance with the views here explained» (p402). Charles Darwin.^[17]

In 1893, Robert Wiedersheim published a book on human anatomy and its relevance to man’s evolutionary history. This book contained a list of 86 human organs that he considered vestigial.^[34] This list included examples such as the appendix and the 3rd molar teeth (wisdom teeth).

The strong grip of a baby is another example.^[35] It is a vestigial reflex, a remnant of the past when pre-human babies clung to their mothers’ hair as the mothers swung through the trees. Human babies’ feet curl up when they are sitting down, while primate babies can grip with their feet as well. All primates except modern man have thick body hair which an infant can grasp, unlike modern humans. The grasp reflex allows the mother to escape danger by climbing a tree using both hands and feet.^[11][36]

Vestigial organs often have some selection against them. The original organs take resources to build and maintain. If they no longer have a function, reducing their size improves fitness. There is direct evidence of selection. Some cave crustacea reproduce more successfully with smaller eyes than do those with larger eyes. This may be because the nervous tissue dealing with sight now becomes available to handle other sensory input.^[37]p310

Embryology[change | change source]

From the eighteenth century, it was known that embryos of different species were much more similar than the adults. In particular, some parts of embryos reflect their evolutionary past. For example, the embryos of land vertebrates develop gill slits like fish embryos. Of course, this is only a temporary stage, which gives rise to many structures in the neck of reptiles, birds, and mammals. The proto-gill slits are part of a complicated system of development: that is why they persisted.^[31]

Another example is the embryonic teeth of baleen whales.^[38] They are later lost. The baleen filter is developed from different tissue, called keratin. Early fossil baleen whales did actually have teeth as well as the baleen.^[39]

A good example is the barnacle. It took many centuries before natural historians discovered that barnacles were crustacea. Their adults look so unlike other crustacea, but their larvae are very similar to those of other crustacea.^[40]

Artificial selection[change | change source]

Charles Darwin lived in a world where animal husbandry and domesticated crops were vitally important. In both cases, farmers selected individuals for breeding that had desirable characteristics and prevented the breeding of individuals with less desirable characteristics. The eighteenth and early nineteenth centuries saw growth in scientific agriculture. Some of that growth was due to artificial breeding.

Darwin discussed artificial selection as a model for natural selection in the 1859 first edition of his work On the Origin of Species, in Chapter IV: Natural selection:

«Slow though the process of selection may be, if feeble man can do much by his powers of artificial selection, I can see no limit to the amount of change… which may be effected in the long course of time by nature’s power of selection».^[9]p109[41]

Nikolai Vavilov showed that rye, originally a weed, came to be a crop plant by unintentional selection. Rye is a tougher plant than wheat: it survives in harsher conditions. Having become a crop like wheat, rye was able to become a crop plant in harsh areas, such as hills and mountains.^[42][43]

There is no real difference in the genetic processes underlying artificial and natural selection, and the concept of artificial selection was used by Charles Darwin as an illustration of the wider process of natural selection. There are practical differences. Experimental studies of artificial selection show that «the rate of evolution in selection experiments is at least two orders of magnitude (that is 100 times) greater than any rate seen in nature or the fossil record».^[44]p157

Artificial new species[change | change source]

Some have thought that artificial selection could not produce new species. It now seems that it can.

New species have been created by domesticated animal husbandry, but the details are not known or not clear. For example, domestic sheep were created by hybridisation, and no longer produce viable offspring with Ovis orientalis, one species from which they are descended.^[45] Domestic cattle, on the other hand, can be considered the same species as several varieties of wild ox, gaur, yak, etc., as they readily produce fertile offspring with them.^[46]

The best-documented new species came from laboratory experiments in the late 1980s. William Rice and G.W. Salt bred fruit flies, Drosophila melanogaster, using a maze with three different choices of habitat such as light/dark and wet/dry. Each generation was put into the maze, and the groups of flies that came out of two of the eight exits were set apart to breed with each other in their respective groups.

After thirty-five generations, the two groups and their offspring were isolated reproductively because of their strong habitat preferences: they mated only within the areas they preferred, and so did not mate with flies that preferred the other areas.^[47][48]

Diane Dodd was also able to show how reproductive isolation can develop from mating preferences in Drosophila pseudoobscura fruit flies after only eight generations using different food types, starch, and maltose.^[49]

Dodd’s experiment has been easy for others to repeat. It has also been done with other fruit flies and foods.^[50]

Observable changes[change | change source]

Some biologists say that evolution has happened when a trait that is caused by genetics becomes more or less common in a group of organisms.^[51] Others call it evolution when new species appear.

Changes can happen quickly in smaller, simpler organisms. For example, many bacteria that cause disease can no longer be killed with some antibiotic medicines. These medicines have only been in use since the 1940s, and at first, they worked extremely well. The bacteria have evolved so that they are less affected by antibiotics.^[52] The drugs killed off all the bacteria except a few which had some resistance. These few resistant bacteria reproduced, and their offspring had the same drug resistance.

The Colorado beetle is famous for its ability to resist pesticides. Over the last 50 years it has become resistant to 52 chemical compounds used in insecticides, including cyanide.^[53] This is natural selection sped up by artificial conditions. However, not every population is resistant to every chemical.^[54] The populations only become resistant to chemicals used in their area.

History[change | change source]

Although there were a number of natural historians in the 18th century who had some idea of evolution, the first well-formed ideas came in the 19th century. Four biologists are considered the most important.

Lamarck[change | change source]

Jean-Baptiste de Lamarck (1744–1829), a French biologist, claimed that animals changed according to natural laws. He said that animals could pass on traits they had acquired during their lifetime to their offspring, using inheritance. Today, his theory is known as Lamarckism. Its main purpose is to explain adaptations by natural means.^[55] He proposed a tendency for organisms to become more complex, moving up a ladder of progress, plus use and disuse.

Lamarck’s idea was that a giraffe’s neck grew longer because it tried to reach higher up. This idea failed because it conflicts with heredity (Mendel’s work). Mendel made his discoveries about half a century after Lamarck’s work.

Darwin[change | change source]

Charles Darwin (1809–1882) wrote his On the Origin of Species in 1859. In this book, he put forward much evidence that evolution had occurred. He also proposed natural selection as the way evolution had taken place. But Darwin did not understand genetics and how traits were actually passed on. He could not accurately explain what made children look like their parents.

Nevertheless, Darwin’s explanation of evolution was fundamentally correct. In contrast to Lamarck, Darwin’s idea was that the giraffe’s neck became longer because those with longer necks survived better.^[17]p177/9 These survivors passed their genes on, and in time the whole species got longer necks.

Wallace[change | change source]

Alfred Russel Wallace OM FRS (1823–1913) was a British naturalist, explorer, biologist, and social activist. He proposed a theory of natural selection at about the same time as Darwin. His idea was published in 1858 together with Charles Darwin’s idea.

Mendel[change | change source]

An Austrian monk called Gregor Mendel (1822–1884) bred plants. In the mid-19th century, he discovered how traits were passed on from one generation to the next.

He used peas for his experiments: some peas have white flowers and others have red ones. Some peas have green seeds and others have yellow seeds. Mendel used artificial pollination to breed the peas. His results are discussed further in Mendelian inheritance. Darwin thought that the inheritance from both parents blended together. Mendel proved that the genes from the two parents stay separate, and may be passed on unchanged to later generations.

Mendel published his results in a journal that was not well-known, and his discoveries were overlooked. Around 1900, his work was rediscovered.^[56][57] Genes are bits of information made of DNA which work like a set of instructions. A set of genes are in every living cell. Together, genes organise the way an egg develops into an adult. With mammals, and many other living things, a copy of each gene comes from the father and another copy from the mother. Some living organisms, including some plants, only have one parent, so get all their genes from them. These genes produce the genetic differences that evolution acts on.

Darwin’s theory[change | change source]

Darwin’s On the Origin of Species has two themes: the evidence for evolution, and his ideas on how evolution took place. This section deals with the second issue.

Variation[change | change source]

The first two chapters of the Origin deal with variations in domesticated plants and animals, and variations in nature.

All living things show variation. Every population which has been studied shows that animals and plants vary as much as humans do.^[58][59]p90 This is a great fact of nature, and without it evolution would not occur. Darwin said that, just as man selects what he wants in his farm animals, so in nature the variations allow natural selection to work.^[60]

The features of an individual are influenced by two things, heredity and environment. First, development is controlled by genes inherited from the parents. Second, living brings its own influences. Some things are entirely inherited, others partly, and some not inherited at all.

The colour of eyes is entirely inherited; they are a genetic trait. Height or weight is only partly inherited, and language is not at all inherited. The fact that humans can speak is inherited, but what language is spoken depends on where a person lives and what they are taught. Another example: a person inherits a brain of somewhat variable capacity. What happens after birth depends on many things such as home environment, education, and other experiences. When a person is an adult, their brain is what their inheritance and life experience have made it.

Evolution only concerns the traits which can be inherited, wholly or partly. The hereditary traits are passed on from one generation to the next through genes. A person’s genes contain all the characteristics that they inherit from their parents. The accidents of life are not passed on. Each person lives a somewhat different life, which increases the differences.

Organisms in any population vary in reproductive success.^[61]p81 From the point of view of evolution, ‘reproductive success’ means the total number of offspring which live to breed and leave offspring themselves.

Inherited variation[change | change source]

Variation can only affect future generations if it is inherited. Because of the work of Gregor Mendel, we know that much variation is inherited. Mendel’s ‘factors’ are now called genes. Research has shown that almost every individual in a sexually reproducing species is genetically unique.^[62]p204

Genetic variation is increased by gene mutations. DNA does not always reproduce exactly. Rare changes occur, and these changes can be inherited. Many changes in DNA cause faults; some are neutral or even advantageous. This gives rise to genetic variation, which is the seed corn of evolution. Sexual reproduction, by the crossing over of chromosomes during meiosis, spreads variation through the population. Other events, like natural selection and drift, reduce variation. A population in the wild always has variation, but the details are always changing.^[59]p90

Natural selection[change | change source]

Evolution mainly works by natural selection. What does this mean? Animals and plants which are best suited to their environment will, on average, survive better. There is a struggle for existence. Those who survive will reproduce and create the next generation. Their genes will be passed on, and the genes of those who did not reproduce will not. This is the basic mechanism which changes the characteristics of a population and causes evolution.

Natural selection explains why living organisms change over time, and explains the anatomy, functions, and behavior that they have. It works like this:

1. All living things have such fertility that their population size could increase rapidly forever.
2. However, population sizes do not increase forever. Mostly, population sizes remain about the same.
3. Food and other resources are limited. Therefore, there is competition for food and resources.
4. No two individuals are alike. Therefore, they will not have the same chances to live and reproduce.
5. Much of this variation can be inherited. Parents pass traits to their children through their genes.
6. The next generation can only come from those that survive and reproduce. After many generations of this, the population will have more helpful genetic differences, and fewer harmful ones.^[63] Natural selection is really a process of elimination.^[1]p117 The elimination is being caused by the relative fit between individuals and the environment they live in.

Selection in natural populations[change | change source]

There are now many cases where natural selection has been proved to occur in wild populations.^[4][64][65] Almost every case investigated of camouflage, mimicry and polymorphism has shown strong effects of selection.^[66]

The force of selection can be much stronger than was thought by the early population geneticists. The resistance to pesticides has grown quickly. Resistance to warfarin in Norway rats (Rattus norvegicus) grew rapidly because those that survived made up more and more of the population. Research showed that, in the absence of warfarin, the resistant homozygote was at a 54% disadvantage to the normal wild type homozygote.^[59]p182[67] This great disadvantage was quickly overcome by the selection for warfarin resistance.

Mammals normally cannot drink milk as adults, but humans are an exception. Milk is digested by the enzyme lactase, which switches off as mammals stop taking milk from their mothers. The human ability to drink milk during adult life is supported by a lactase mutation which prevents this switch-off. Human populations have a high proportion of this mutation wherever milk is important in the diet. The spread of this ‘milk tolerance’ is promoted by natural selection, because it helps people survive where milk is available. Genetic studies suggest that the oldest mutations causing lactase persistence only reached high levels in human populations in the last ten thousand years.^[68][69] Therefore, lactase persistence is often cited as an example of recent human evolution.^[70][71] As lactase persistence is genetic, but animal husbandry a cultural trait, this is gene–culture coevolution.^[72]

Adaptation[change | change source]

Adaptation is one of the basic phenomena of biology.^[73] Through the process of adaptation, an organism becomes better suited to its habitat.^[74]

Adaptation is one of the two main processes that explain the diverse species we see in biology. The other is speciation (species-splitting or cladogenesis).^[75][76] A favourite example used today to study the interplay of adaptation and speciation is the evolution of cichlid fish in African rivers and lakes.^[77][78]

When people speak about adaptation they often mean something which helps an animal or plant survive. One of the most widespread adaptations in animals is the evolution of the eye. Another example is the adaptation of horses’ teeth to grinding grass. Camouflage is another adaptation; so is mimicry. The better-adapted animals are the most likely to survive and reproduce successfully (natural selection).

An internal parasite (such as a fluke) is a good example: it has a very simple bodily structure, but still the organism is highly adapted to its particular 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, which is often quite complex.^[79]

Limitations[change | change source]

Not all features of an organism are adaptations.^[59]p251 Adaptations tend to reflect the past life of a species. If a species has recently changed its life style, a once valuable adaptation may become useless, and eventually become a dwindling vestige.

Adaptations are never perfect. There are always tradeoffs between the various functions and structures in a body. It is the organism as a whole that lives and reproduces, therefore it is the complete set of adaptations that is passed on to future generations.

Genetic drift and its effect[change | change source]

In populations, there are forces that add variation to the population (such as mutation), and forces that remove it. Genetic drift is the name given to random changes which remove variation from a population. Genetic drift gets rid of variation at the rate of 1/(2N) where N = population size.^[44]p29 It is therefore «a very weak evolutionary force in large populations».^[44]p55

Genetic drift explains how random chance can affect evolution in surprisingly big ways, but only when populations are quite small. Overall, its action is to make the individuals more similar to each other, and hence more vulnerable to disease or to chance events in their environment.

1. Drift reduces genetic variation in populations, potentially reducing a population’s ability to survive new selective pressures.
2. Genetic drift acts faster and has more drastic results in smaller populations. Small populations usually become extinct.
3. Genetic drift may contribute to speciation (starting a new species) if the small group does survive.
4. Bottleneck events: when a large population is suddenly and drastically reduced in size by some event, the genetic variety will be very much reduced. Infections and extreme climate events are frequent causes. Occasionally, invasions by more competitive species can be devastating.^[80]
   ♦ In late 1800s, hunting reduced the Northern elephant seal to only about 20 individuals. Although the population has rebounded, its genetic variability is much less than that of the Southern elephant seal.
   ♦ Cheetahs have very little variation. We think the species was reduced to a small number at some recent time. Because it lacks genetic variation, it is in danger of infectious diseases.^[81]
5. Founder events: these occur when a small group buds off from a larger population. The small group then lives separately from the main population. The human species is often quoted as having been through such stages. For example, when groups left Africa to set up elsewhere (see human evolution). Apparently, we have less variation than would be expected from our worldwide distribution.
   Groups that arrive on islands far from the mainland are also good examples. These groups, by virtue of their small size, cannot carry the full range of alleles to be found in the parent population.^[82][83]

Species[change | change source]

How species form is a major part of evolutionary biology. Darwin interpreted ‘evolution’ (a word he did not use at first) as being about speciation. That is why he called his famous book On the Origin of Species.

Darwin thought most species arose directly from pre-existing species. This is called anagenesis: new species by older species changing. Now we think most species arise by previous species splitting: cladogenesis.^[84][85]

Species splitting[change | change source]

Two groups that start the same can become very different if they live in different places. When a species gets split into two geographical regions, a process starts. Each adapts to its own situation. After a while, individuals from one group can no longer reproduce with the other group. Two separate species have evolved from one.

A German explorer, Moritz Wagner, during his three years in Algeria in the 1830s, studied flightless beetles. Each species is confined to a stretch of the north coast between rivers which descend from the Atlas mountains to the Mediterranean. As soon as one crosses a river, a different but closely related species appears.^[86] He wrote later:

«… a [new] species will only [arise] when a few individuals [cross] the limiting borders of their range… the formation of a new race will never succeed… without a long continued separation of the colonists from the other members of their species».^[87]

This was an early account of the importance of geographical separation. Another biologist who thought geographical separation was critical was Ernst Mayr.^[88]

One example of natural speciation is the three-spined stickleback, a sea fish that, after the last ice age, invaded freshwater, and set up colonies in isolated lakes and streams. Over about 10,000 generations, the sticklebacks show great differences, including variations in fins, changes in the number or size of their bony plates, variable jaw structure, and colour differences.^[89]

The wombats of Australia fall into two main groups, common wombats and hairy-nosed wombats. The two types look very similar, apart from the hairiness of their noses. However, they are adapted to different environments. Common wombats live in forested areas and eat mostly green food with lots of moisture. They often feed in the daytime. Hairy-nosed wombats live on hot dry plains where they eat dry grass with very little water or nutrition in it. Their metabolic rate is slow and they sleep most of the day underground.

When two groups that started the same become different enough, then they become two different species. Part of the theory of evolution is that all living things started the same, but then split into different groups over billions of years.^[90]

Modern evolutionary synthesis[change | change source]

This was an important movement in evolutionary biology, which started in the 1930s and finished in the 1950s.^[91][92] It has been updated regularly ever since.
The synthesis explains how the ideas of Charles Darwin fit with the discoveries of Gregor Mendel, who found out how we inherit our genes. The modern synthesis brought Darwin’s idea up to date. It bridged the gap between different types of biologists: geneticists, naturalists, and palaeontologists.

When the theory of evolution was developed, it was not clear that natural selection and genetics worked together. But Ronald Fisher showed that natural selection would work to change species.^[93] Sewall Wright explained genetic drift in 1931.^[94]

• Evolution and genetics: evolution can be explained by what we know about genetics, and what we see of animals and plants living in the wild.^[91][92]
• Thinking in terms of populations, rather than individuals, is important. The genetic variety existing in natural populations is a key factor in evolution.^[95]
• Evolution and fossils: the same factors which act today also acted in the past.^[96]
• Gradualism: evolution is gradual, and usually takes place by small steps. There are some exceptions to this, notably polyploidy, especially in plants.^[97][98]
• Natural selection: the struggle for existence of animals and plants in the wild causes natural selection. The strength of natural selection in the wild was greater than even Darwin expected.^[65]
• Genetic drift can be important in small populations.^[44]
• The rate of evolution can vary. There is very good evidence from fossils that different groups can evolve at different rates, and that different parts of an animal can evolve at different rates.^{[59]p292, 397}

Some areas of research[change | change source]

Co-evolution[change | change source]

Co-evolution is where the existence of one species is tightly bound up with the life of one or more other species.

New or ‘improved’ adaptations which occur in one species are often followed by the appearance and spread of related features in the other species. The life and death of living things is intimately connected, not just with the physical environment, but with the life of other species.

These relationships may continue for millions of years, as it has in the pollination of flowering plants by insects.^[99][100] The gut contents, wing structures, and mouthparts of fossilized beetles and flies suggest that they acted as early pollinators. The association between beetles and angiosperms during the Lower Cretaceous period led to parallel radiations of angiosperms and insects into the late Cretaceous. The evolution of nectaries in Upper Cretaceous flowers signals the beginning of the mutualism between hymenoptera and angiosperms.^[101]

Tree of life[change | change source]

Charles Darwin was the first to use this metaphor in biology. The evolutionary tree shows the relationships among various biological groups. It includes data from DNA, RNA and protein analysis. Tree of life work is a product of traditional comparative anatomy, and modern molecular evolution and molecular clock research.

The major figure in this work is Carl Woese, who defined the Archaea, the third domain (or kingdom) of life.^[102] Below is a simplified version of present-day understanding.^[103]

Macroevolution[change | change source]

Macroevolution: the study of changes above the species level, and how they take place. The basic data for such a study are fossils (palaeontology) and the reconstruction of ancient environments. Some subjects whose study falls within the realm of macroevolution:

• Adaptive radiation, such as the Cambrian Explosion.
• Changes in biodiversity through time.
• Mass extinctions.
• Speciation and extinction rates.
• The debate between punctuated equilibrium and gradualism.
• The role of development in shaping evolution: heterochrony; hox genes.
• Origin of major categories: cleidoic egg; origin of birds.

It is a term of convenience: for most biologists it does not suggest any change in the process of evolution.^{[4][104][105]p87} For some palaeontologists, what they see in the fossil record cannot be explained just by the gradualist evolutionary synthesis.^[106] They are in the minority.

Altruism and group selection[change | change source]

Altruism – the willingness of some to sacrifice themselves for others – is widespread in social animals. As explained above, the next generation can only come from those who survive and reproduce. Some biologists have thought that this meant altruism could not evolve by the normal process of selection. Instead a process called «group selection» was proposed.^[107][108] Group selection refers to the idea that alleles can become fixed or spread in a population because of the benefits they bestow on groups, regardless of the alleles’ effect on the fitness of individuals within that group.

For several decades, critiques cast serious doubt on group selection as a major mechanism of evolution.^{[109][110][111][112]}

In simple cases it can be seen at once that traditional selection suffices. For example, if one sibling sacrifices itself for three siblings, the genetic disposition for the act will be increased. This is because siblings share on average 50% of their genetic inheritance, and the sacrificial act has led to greater representation of the genes in the next generation.

Altruism is now generally seen as emerging from standard selection.^{[113][114][115][116][117]} The warning note from Ernst Mayr, and the work of William Hamilton are both important to this discussion.^[118][119]

Hamilton’s equation[change | change source]

Hamilton’s equation describes whether or not a gene for altruistic behaviour will spread in a population. The gene will spread if rxb is greater than c:

where:

Sexual reproduction[change | change source]

Main article: Sex

At first, sexual reproduction might seem to be at a disadvantage compared with asexual reproduction. In order to be advantageous, sexual reproduction (cross-fertilisation) has to overcome a two-fold disadvantage (takes two to reproduce) plus the difficulty of finding a mate. Why, then, is sex so nearly universal among eukaryotes? This is one of the oldest questions in biology.^[120]

The answer has been given since Darwin’s time: because the sexual populations adapt better to changing circumstances. A recent laboratory experiment suggests this is indeed the correct explanation.^[121][122]

«When populations are outcrossed^[123] genetic recombination occurs between different parental genomes. This allows beneficial mutations to escape deleterious alleles on its original background, and to combine with other beneficial alleles that arise elsewhere in the population. In selfing^[124] populations, individuals are largely homozygous and recombination has no effect».^[121]

In the main experiment, nematode worms were divided into two groups. One group was entirely outcrossing, the other was entirely selfing. The groups were subjected to a rugged terrain and repeatedly subjected to a mutagen.^[125] After 50 generations, the selfing population showed a substantial decline in fitness (= survival), whereas the outcrossing population showed no decline. This is one of a number of studies that show sexuality to have real advantages over non-sexual types of reproduction.^[126]

What evolution is used for today[change | change source]

An important activity is artificial selection for domestication. This is when people choose which animals to breed from, based on their traits. Humans have used this for thousands of years to domesticate plants and animals.^[127]

More recently, it has become possible to use genetic engineering. New techniques such as ‘gene targeting’ are now available. The purpose of this is to insert new genes or knock out old genes from the genome of a plant or animal. A number of Nobel Prizes have already been awarded for this work.

However, the real purpose of studying evolution is to explain and help our understanding of biology. After all, it is the first good explanation of how living things came to be the way they are. That is a big achievement. The practical things come mostly from genetics, the science started by Gregor Mendel, and from molecular and cell biology.

Evolution gems[change | change source]

In 2010 the journal Nature selected 15 topics as ‘Evolution gems’. These were:

Gems from the fossil record[change | change source]

1. Land-living ancestors of whales
2. From water to land (see tetrapod)
3. The origin of feathers (see origin of birds)
4. The evolutionary history of teeth
5. The origin of vertebrate skeleton

Gems from habitats[change | change source]

1. Natural selection in speciation
2. Natural selection in lizards
3. A case of co-adaptation
4. Differential dispersal in wild birds
5. Selective survival in wild guppies
6. Evolutionary history matters

Gems from molecular processes[change | change source]

1. Darwin’s Galapagos finches
2. Microevolution meets macroevolution
3. Toxin resistance in snakes and clams
4. Variation versus stability

• Nature is the oldest scientific weekly journal. The link downloads as a free text file, complete with references. The idea is to make the information available to teachers.^[128]

Responses to the idea of evolution[change | change source]

Debates about the fact of evolution[change | change source]

The idea that all life evolved had been proposed before Charles Darwin published On the Origin of species. Even today, some people still discuss the concept of evolution and what it means to them, their philosophy, and their religion. Evolution does explain some things about our human nature.^[130] People also talk about the social implications of evolution, for example in sociobiology.

Some people have the religious belief that life on Earth was created by a god. In order to fit in the idea of evolution with that belief, people have used ideas like guided evolution or theistic evolution. They say that evolution is real, but is being guided in some way.^{[15][131][132][133]}

There are many different concepts of theistic evolution. Many creationists believe that the creation myth found in their religion goes against the idea of evolution.^[134] As Darwin realised, the most controversial part of the evolutionary thought is what it means for human origins.

In some countries, especially in the United States, there is tension between people who accept the idea of evolution and those who do not accept it. The debate is mostly about whether evolution should be taught in schools, and in what way this should be done.^[135]

Other fields, like cosmology^[136] and earth science^[137] also do not match with the original writings of many religious texts. These ideas were once also fiercely opposed. Death for heresy was threatened to those who wrote against the idea that Earth was the center of the universe.

Evolutionary biology is a more recent idea. Certain religious groups oppose the idea of evolution more than other religious groups do. For instance, the Roman Catholic Church now has the following position on evolution: Pope Pius XII said in his encyclical Humani Generis published in the 1950s:

«The Church does not forbid that (…) research and discussions (..) take place with regard to the doctrine of evolution, in as far as it inquires into the origin of the human body as coming from pre-existent and living matter,» Pope Pius XII Humani Generis^[138]

Pope John Paul II updated this position in 1996. He said that Evolution was «more than a hypothesis»:

«In his encyclical Humani Generis, my predecessor Pius XII has already [said] that there is no conflict between evolution and the doctrine of the faith regarding man and his vocation. (…) Today, more than a half-century after (..) that encyclical, some new findings lead us toward the recognition of evolution as more than an hypothesis. In fact it is remarkable that this theory has had progressively greater influence on the spirit of researchers, following a series of discoveries in different scholarly disciplines,» Pope John Paul II speaking to the Pontifical Academy of Science^[139]

The Anglican Communion also does not oppose the scientific account of evolution.

Using evolution for other purposes[change | change source]

Many of those who accepted evolution were not much interested in biology. They were interested in using the theory to support their own ideas on society.

Racism[change | change source]

Some people have tried to use evolution to support racism. People wanting to justify racism claimed that certain groups, such as black people, were inferior. In nature, some animals do survive better than others, and it does lead to animals better adapted to their circumstances. With humans groups from different parts of the world, all evolution can say is that each group is probably well suited to its original situation. Evolution makes no judgements about better or worse. It does not say that any human group is superior to any other.^[140]

Eugenics[change | change source]

The idea of eugenics was rather different. Two things had been noticed as far back as the 18th century. One was the great success of farmers in breeding cattle and crop plants. They did this by selecting which animals or plants would produce the next generation (artificial selection). The other observation was that lower class people had more children than upper-class people. If (and it’s a big if) the higher classes were there on merit, then their lack of children was the exact reverse of what should be happening. Faster breeding in the lower classes would lead to the society getting worse.

The idea to improve the human species by selective breeding is called eugenics. The name was proposed by Francis Galton, a bright scientist who meant to do good.^[141] He said that the human stock (gene pool) should be improved by selective breeding policies. This would mean that those who were considered «good stock» would receive a reward if they reproduced. However, other people suggested that those considered «bad stock» would need to undergo compulsory sterilization, prenatal testing and birth control. The German Nazi government (1933–1945) used eugenics as a cover for their extreme racial policies, with dreadful results.^[142]

The problem with Galton’s idea is how to decide which features to select. There are so many different skills people could have, you could not agree who was «good stock» and who was «bad stock». There was rather more agreement on who should not be breeding. Several countries passed laws for the compulsory sterilisation of unwelcome groups.^[143] Most of these laws were passed between 1900 and 1940. After World War II, disgust at what the Nazis had done squashed any more attempts at eugenics.

Algorithm design[change | change source]

Some equations can be solved using algorithms that simulate evolution. Evolutionary algorithms work like that.

[change | change source]

Another example of using ideas about evolution to support social action is social Darwinism. Social Darwinism is a term given to the ideas of the 19th century social philosopher Herbert Spencer. Spencer believed the survival of the fittest could and should be applied to commerce and human societies as a whole.

Again, some people used these ideas to claim that racism, and ruthless economic policies were justified.^[144] Today, most biologists and philosophers say that the theory of evolution should not be applied to social policy.^[145][146]

Controversy[change | change source]

Some people disagree with the idea of evolution. They disagree with it for a number of reasons. Most often these reasons are influenced by or based on their religious beliefs instead of science. People who do not agree with evolution usually believe in creationism or intelligent design.

Despite this, evolution is one of the most successful theories in science. People have discovered it to be useful for different kinds of research. None of the other suggestions explain things, such as fossil records, as well. So, for almost all scientists, evolution is not in doubt.^{[2][147][148][149]}

Further reading[change | change source]

Evidence for evolution[change | change source]

These books are mostly about the evidence for evolution.

• Coyne, Jerry A. 2009 Why evolution is true. Oxford University Press, Oxford. ISBN 0670-02053-2 (pbk)
• Dawkins, Richard 2009. The greatest show on Earth. Bantam, London. ISBN 978-0-593-06173-2 (hbk)
• Futuyma D.J. 1983. Science on trial: the case for evolution. Pantheon Books, New York. ISBN 0-394-52371-7; 2nd ed 1995 Sinauer Associates, Sunderland, Massachusetts. ISBN 0-87893-184-8.
• Prothero, Donald R. 2007. Evolution: what the fossils say and why it matters. Columbia University Press, New York. ISBN 978-0-231-13962-5 (hbk)

The process of evolution[change | change source]

These books cover most evolutionary topics.

• Barton N.H; Briggs D.E.G; Eisen J.A; Goldstein D.B. & Patel N.H. 2007. Evolution. New York: Cold Spring Harbor Laboratory Press. ISBN 978-0-879-69684-9. Strong in molecular evolution; brings together molecular biology with evolutionary concepts.
• Futuyma D.J. 1979. Evolutionary biology. 1st ed. Sinauer Associates, Sunderland, Massachusetts. ISBN 0-87893-199-6; 2nd ed 1986 Sinauer. ISBN 0-87893-188-0; 3rd ed 1998 Sinauer. ISBN 0-87893-189-9. Widely used textbook, available second-hand. For students and teachers.
• Futuyma D.J. 2005. Evolution. Sinauer Associates, Sunderland, Massachusetts. ISBN 0-87893-187-2; 2nd ed 2009 Sinauer. ISBN 978-0-87893-223-8. Successor to above; but basically a different book. For students and teachers.
• Freeman, Scott & Herron, Jon; 1997. Evolutionary analysis. Prentice Hall ISBN 0-13-568023-9; 2nd ed 2000 ISBN 0-13-017291-X; 3rd ed 2004 Cummings ISBN 978-0-13-101859-4; 4th ed 2007 Cummings ISBN 0-13-227584-8. Modern topics such as phylogenetic trees based on genomics, genetics, molecular biology. Has website: [4] Archived 2012-12-15 at the Wayback Machine For students and teachers.
• Ridley, Mark 1993. Evolution. Blackwell ISBN 0-86542-226-5; 2nd ed 1996 Wiley-Blackwell ISBN 0-86542-495-0; 3rd ed 2003 Wiley ISBN 978-1-4051-0345-9. Comprehensive: case studies, commentary, dedicated website and CD. For students and teachers.
• Mayr, Ernst. 2001. What evolution is. Weidenfeld & Nicolson, London. ISBN 0-297-60741-3. Clearly written, for a general audience.

[change | change source]

• Evolutionary biology
• Coevolution
• Human evolution
• Adaptation
• Natural selection
• Sociobiology

References[change | change source]

Other websites[change | change source]

• Video (1980; Cosmos animation; 8:01): «Evolution» – Carl Sagan at YouTube
• Understanding Evolution — a guide prepared by the University of California, Berkeley
• Darwin Online Darwin’s publications; papers and bibliography; biographies and reviews.
• Talk Origins in depth website on information about evolution and the evidence for it
• National Center for Science Education Information on how evolution works
• Article about evolution — PBS

Last Updated:
14 Apr 2023
— Updated example sentences

Content

• What is Evolution:
• Evolution in biology
• Theory of the evolution of species
• Convergent and divergent evolution
• Evolutionism or social evolutionism

What is Evolution:

Evolution is the change that occurs from one state to another in an object or subject, as a product of a process of progressive transformation. It can refer to genetic changes in a species, the development of a person (biological or qualitative), the progression of historical stages, the phases of a situation or the transformation of an object and of nature in general.

Etymologically, the word evolution comes from the Latin expression evolutionary, formed by the contraction of the word former, which means ‘out’, with the conjugation of the verb I will be back, which means ‘to go around’.

Some synonyms or terms related to evolution They are: transformation, development, variation, alteration, change, growth, advancement, improvement, movement or progress.

The word is frequently used to refer to the qualitative improvement of a person, situation, historical context, object, etc. Therefore, expressions such as personal evolution, technological evolution, scientific evolution, economic evolution, etc. are common.

Evolution in biology

In biology, evolution is specifically related to the study of the transformation processes of species, that is, the processes of adaptation and genetic mutation that generate structural changes in living beings. In other words, the concept of evolution in nature is defined as the changes in the genetic records of a biological population (animal or plant) through generations.

Theory of the evolution of species

The theory of the evolution of species was presented by Charles R. Darwin and Alfred Wallace in 1859, in a book entitled The origin of species. It was preceded by the investigations and theories of Lamarck, who had already pointed conclusions in that direction.

According to the authors, the human (homo sapiens) is the result of the evolution of other species such as homo erectus and the homo habilis, a statement that challenged the creation theory prevailing in the nineteenth century. Darwin also postulated that the evolution of species was the result of natural selection and adaptation.

Today, there are different hypotheses on the table about the causes of evolution. These are:

1. Natural selection: theory of evolution by natural selection and adaptation (Darwin’s thesis).
2. Population reduction: less variety of genes.
3. The way of reproduction: which gene reproduces the most.
4. Genetic mutation: one type of gene is shortened.
5. Gene flow: migration of genes to other places.

See more details on the Theory of Evolution.

Convergent and divergent evolution

In the study of the evolution of species we speak of convergent and divergent evolution. Convergent evolution occurs when two species of different phylogenetic origin, evolve to generate similar structures or elements. For example: both hummingbirds and butterflies developed the same type of tongue to extract nectar from flowers.

Divergent evolution is one in which species with a common origin but that have been separated, evolve unevenly to adapt quickly to environmental conditions, either through mutations or natural selection. for example, those mammals that resulted from reptiles and developed limbs to adapt to a new ecosystem. Some of them turned two of their limbs into arms, like apes, and others kept their limbs as legs.

Evolutionism or social evolutionism

In general terms, the expressions are used social evolution or cultural evolution to refer to the different transformation processes that societies or cultures undergo.

However, there are specific analytical approaches that analyze societies from an evolutionary point of view, that is, from the paradigm of evolution proper to scientific studies. We talk about social evolutionism and, more specifically, of darwinism.

According to these approaches, sociocultural evolution would have to be analyzed from the law of natural selection (survival of the fittest), which would explain why some civilizations prevail over others.

Historically, these theories have functioned as an ideological justification for Western domination over the world, which gives it an ethnocentric and Eurocentric character, today widely refuted.

Hence, there may still be an evaluative and even ideological use of the word evolution. For example, when the word is used to make comparisons of superiority / inferiority: «The current state of the country demands that we review the experiences of the most evolved countries.»

In the anthropology of the last decades, cultural relativism has proposed new methods to study social changes, from the recognition that each society / culture is unique and has particularities that deserve attention. These methods reject social evolutionism for its ethnocentric character.

See also

• Cultural relativism
• Darwinism.
• Social evolutionism