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Default zoology paper 2 (part B)

Evolution

Evolution (also known as biological, genetic or organic evolution) is the change in the inherited traits of a population of organisms through successive generations.[1] This change results from interactions between processes that introduce variation into a population, and other processes that remove it. As a result, variants with particular traits become more, or less, common. A trait is a particular characteristic—anatomical, biochemical or behavioural—that is the result of gene–environment interaction.

The main source of variation is mutation, which introduces genetic changes. These changes are heritable (can be passed on through reproduction), and may give rise to alternative traits in organisms. Another source of variation is genetic recombination, which shuffles the genes into new combinations which can result in organisms exhibiting different traits. Under certain circumstances, variation can also be increased by the transfer of genes between species,[2][3] and by the extremely rare, but significant, wholesale incorporation of genomes through endosymbiosis.[4][5]

Two main processes cause variants to become more common or rarer in a population. One is natural selection, through which traits that aid survival and reproduction become more common, while traits that hinder survival and reproduction become rarer. Natural selection occurs because only a small proportion of individuals in each generation will survive and reproduce, since resources are limited and organisms produce many more offspring than their environment can support. Over many generations, heritable variation in traits is filtered by natural selection and the beneficial changes are successively retained through differential survival and reproduction. This iterative process adjusts traits so they become better suited to an organism's environment: these adjustments are called adaptations.[6]

However, not all change is adaptive. Another cause of evolution is genetic drift, which leads to random changes in how common traits are in a population. Genetic drift is most important when traits do not strongly influence survival—particularly so in small populations, in which chance plays a disproportionate role in the frequency of traits passed on to the next generation.[7][8] Genetic drift is important in the neutral theory of molecular evolution, and plays a role in the molecular clocks that are used in phylogenetic studies.

A key process in evolution is speciation, in which a single ancestral species splits and diversifies into multiple new species. There are several modes through which this occurs. Ultimately, all living (and extinct) species are descended from a common ancestor via a long series of speciation events. These events stretch back in a diverse "tree of life" which has grown over the 3.5 billion years during which life has existed on Earth.[9][10][11][12] This is visible in anatomical, genetic and other similarities between groups of organisms, geographical distribution of related species, the fossil record and the recorded genetic changes in living organisms over many generations.

Evolutionary biologists document the fact that evolution occurs, and also develop and test theories which explain its causes. The study of evolutionary biology began in the mid-nineteenth century, when research into the fossil record and the diversity of living organisms convinced most scientists that species changed over time.[13] The mechanism driving these changes remained unclear until the theory of natural selection was independently proposed by Charles Darwin and Alfred Wallace. In 1859, Darwin's seminal work On the Origin of Species brought the new theory of evolution by natural selection to a wide audience,[14] leading to the overwhelming acceptance of evolution among scientists.[15][16][17][18]

In the 1930s, Darwinian natural selection became understood in combination with Mendelian inheritance, forming the modern evolutionary synthesis,[19] which connected the substrate of evolution (inherited genetics) and the mechanism of evolution (natural selection). This powerful explanatory and predictive theory has become the central organizing principle of modern biology, directing research and providing a unifying explanation for the history and diversity of life on Earth.[16][17][20] Evolution is applied and studied in fields as diverse as agriculture, anthropology, conservation biology, ecology, medicine, paleontology, philosophy, and psychology along with other specific topics in the previous listed fields.
History of evolutionary thought

The roots of naturalistic thinking on biology can be dated to at least the 6th century BCE, with the Greek philosopher Anaximander.[21]

Early Christian Church Fathers and Medieval European scholars treated the Genesis creation myth as allegory and believed that natural organisms were unstable and capricious, but the Protestant Reformation inspired Biblical literalism and a natural theology in which species were static and fixed.

As emerging science explored mechanical philosophy in the 18th century, proto-evolutionary ideas were set out by a few natural philosophers such as Pierre Maupertuis in 1745 and Erasmus Darwin in 1796.[22]

The word evolution itself (from the Latin evolutio, meaning "to unroll like a scroll") was initially used to refer to embryological development; its first use in relation to development of species came in 1762, when Charles Bonnet used it for his concept of "pre-formation", in which females carried a miniature form of all future generations. The term gradually gained a more general meaning of growth or progressive development.[23] The first published modern use of the word has been attributed to the Edinburgh New Philosophical Journal in 1826, edited by Robert Jameson but arguably authored by Robert Edmond Grant.[24]

The Bible-based Ussher chronology of the 1650s had calculated creation at 4004 BC, but by the 1780s geologists assumed a much older world. Wernerians thought strata were deposits from shrinking seas, but James Hutton proposed a self-maintaining infinite cycle. Georges Cuvier's paleontological work in the 1790s established the reality of extinction, which he explained by local catastrophes, followed by repopulation of the affected areas by other species. He held that species were fixed, and marginalised the ideas of the biologist Jean-Baptiste Lamarck about transmutation of species which were only taken up by radicals.

Geologists such as Adam Sedgwick adapted Cuvier's catastrophism to show repeated worldwide annihilation and creation of new fixed species adapted to a changed environment, initially identifying the most recent catastrophe as the biblical flood. In opposition to this view, Charles Lyell adapted Hutton's concept into a stricter uniformitarianism which strongly influenced the young geologist Charles Darwin during the Beagle expedition. Darwin initially followed Lyell's idea of repeated "centres of creation" of fixed species, but questioned Lyell's views and in 1836, near the end of the voyage, he expressed doubts that species were fixed. Darwin formulated his idea of natural selection in 1838 and was still developing his theory in 1858 when Alfred Russel Wallace sent him a similar theory, and both were presented to the Linnean Society of London in separate papers.[25] At the end of 1859, Darwin's publication of On the Origin of Species explained natural selection in detail and presented evidence leading to increasingly wide acceptance of the occurrence of evolution.

Debate about the mechanisms of evolution continued, and Darwin could not explain the source of the heritable variations which would be acted on by natural selection.[26] Like Lamarck, he still thought that parents passed on adaptations acquired during their lifetimes,[27] a theory which was subsequently dubbed Lamarckism.[28] In the 1880s, August Weismann's experiments indicated that changes from use and disuse were not heritable, and Lamarckism gradually fell from favour.[29][30] More significantly, Darwin could not account for how traits were passed down from generation to generation. In 1865 Gregor Mendel found that traits were inherited in a predictable manner.[31] When Mendel's work was rediscovered in the 1900s, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution.

Yet it was the rediscovery of Gregor Mendel's pioneering work on the fundamentals of genetics (of which Darwin and Wallace were unaware) by Hugo de Vries and others in the early 1900s that provided the impetus for a better understanding of how variation occurs in plant and animal traits. That variation is the main fuel used by natural selection to shape the wide variety of adaptive traits observed in organic life. Even though Hugo de Vries and other early geneticists rejected gradual natural selection, their rediscovery of and subsequent work on genetics eventually provided a solid basis on which the theory of evolution stood even more convincingly than when it was originally proposed.[32]

The apparent contradiction between Darwin's theory of evolution by natural selection and Mendel's work was reconciled in the 1920s and 1930s by evolutionary biologists such as J.B.S. Haldane, Sewall Wright, and particularly Ronald Fisher, who set the foundations for the establishment of the field of population genetics. The end result was a combination of evolution by natural selection and Mendelian inheritance, the modern evolutionary synthesis.[33] In the 1940s, the identification of DNA as the genetic material by Oswald Avery and colleagues and the subsequent publication of the structure of DNA by James Watson and Francis Crick in 1953, demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become core parts of evolutionary biology and have revolutionised the field of phylogenetics.[19]

In its early history, evolutionary biology primarily drew in scientists from traditional taxonomically oriented disciplines, whose specialist training in particular organisms addressed general questions in evolution. As evolutionary biology expanded as an academic discipline, particularly after the development of the modern evolutionary synthesis, it began to draw more widely from the biological sciences.[19] Currently the study of evolutionary biology involves scientists from fields as diverse as biochemistry, ecology, genetics and physiology, and evolutionary concepts are used in even more distant disciplines such as psychology, medicine, philosophy and computer science.

In the 21st century, current research in evolutionary biology deals with several areas where the modern evolutionary synthesis may need modification or extension, such as assessing the relative importance of various ideas on the unit of selection and evolvability and how to fully incorporate the findings of evolutionary developmental biology.[34][35]
Heredity

Evolution in organisms occurs through changes in heritable traits – particular 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.[36] Inherited traits are controlled by genes and the complete set of genes within an organism's genome is called its genotype.[37]

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.[38] 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 their genotype; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.[39]

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information.[37] DNA is a long polymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence.

Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.

However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by multiple interacting genes.[40][41] The study of such complex traits is a major area of current genetic research. Another unsolved question in genetics is whether or not epigenetics is important in evolution. Epigenetics is when a trait is inherited without there being any change in gene sequences.[42]
Variation

An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes.[41] The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when a new allele reaches the point of fixation — when it either disappears from the population or replaces the ancestral allele entirely.[43]

Variation comes from mutations in genetic material, migration between populations (gene flow), and the reshuffling of genes through sexual reproduction. Variation also comes from exchanges of genes between different species; for example, through horizontal gene transfer in bacteria, and hybridisation in plants.[44] Despite the constant introduction of variation through these processes, most of the genome of a species is identical in all individuals of that species.[45] However, even relatively small changes in genotype can lead to dramatic changes in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.[46]
Mutation

Random mutations constantly occur in the genomes of organisms; these mutations create genetic variation. Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication.[47][48][49] These mutations involve several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[50]

Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations.[47] Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.[51] Viruses that use RNA as their genetic material have rapid mutation rates,[52] which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system.[53]

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.[54] Extra copies of genes are a major source of the raw material needed for new genes to evolve.[55] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.[56] 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.[57]

New genes can be created 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.[58][59] Other types of mutation can even create entirely new genes from previously noncoding DNA.[60][61]

The creation 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.[62][63] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together creating new combinations with new and complex functions.[64] For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyze one step in the overall process, like a step in an assembly line.[65]

Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, two chromosomes in the Homo genus fused to produce human chromosome 2; this fusion did not occur in the lineage of the other apes, and they retain these separate chromosomes.[66] In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by making populations less likely to interbreed, and thereby preserving genetic differences between these populations.[67]

Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes.[68] For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been recruited to perform functions such as regulating gene expression.[69] Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.[48]
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.[70] 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.[71] Sex usually increases genetic variation and may increase the rate of evolution.[72][73] However, asexuality is advantageous in some environments as it can evolve in previously sexual animals.[74] Here, asexuality might allow the two sets of alleles in their genome to diverge and gain different functions.[75]

Recombination allows even alleles that are close together in a strand of DNA to be inherited independently. 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.[76] This tendency is measured by finding how often two alleles occur together on a single chromosome, 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.[77]

When alleles cannot be separated by recombination – such as in mammalian Y chromosomes, which pass intact from fathers to sons – harmful mutations accumulate.[78][79] By breaking up allele combinations, sexual reproduction allows the removal of harmful mutations and the retention of beneficial mutations.[80] In addition, recombination and reassortment can produce individuals with new and advantageous gene combinations. These positive effects are balanced by the fact that sex reduces an organism's reproductive rate, can cause mutations and may separate beneficial combinations of genes.[80] The reasons for the evolution of sexual reproduction are therefore unclear and this question is still an active area of research in evolutionary biology,[81][82] that has prompted ideas such as the Red Queen hypothesis.[83]
Population genetics

From a genetic viewpoint, evolution is a generation-to-generation change in the frequencies of alleles within a population that shares a common gene pool.[84] A population is a localised group of individuals belonging to the same species. For example, all of the moths of the same species living in an isolated forest represent a population. A single gene in this population may have several alternate forms, which account for variations between the phenotypes of the organisms. An example might be a gene for colouration in moths that has two alleles: black and white.

A gene pool is the complete set of alleles for a gene in a single population; the allele frequency measures the fraction of the gene pool composed of a single allele (for example, what fraction of moth colouration genes are the black allele). Evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms; for example, the allele for black colour in a population of moths becoming more common.

To understand the mechanisms that cause a population to evolve, it is useful to consider what conditions are required for a population not to evolve. The Hardy-Weinberg principle states that the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilisation.[85] Such a population is said to be in Hardy-Weinberg equilibrium; it is not evolving.[86]
Gene flow

Gene flow is the exchange of genes between populations, which are usually of the same species.[88] Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer.

Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. As barriers to reproduction between two diverging populations are required for the populations to become new species, gene flow may slow this process by spreading genetic differences between the populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes.[89]

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.[90] Such hybrids are generally infertile, due to the two different sets of chromosomes being unable to pair up during meiosis. 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.[91] The importance of hybridisation in creating new species of animals is unclear, although cases have been seen in many types of animals,[92] with the gray tree frog being a particularly well-studied example.[93]

Hybridisation is, however, an important means of speciation in plants, since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals.[94][95] Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis.[96] Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations.[97]

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.[98] 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.[99] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred.[100][101] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants.[102] Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.[103] Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and mitochondria.[104]
Mechanisms

The two main mechanisms that produce evolution are natural selection and genetic drift. Natural selection is the process which favors genes that aid survival and reproduction. Genetic drift is the random change in the frequency of alleles, caused by the random sampling of a generation's genes during reproduction. The relative importance of natural selection and genetic drift in a population varies depending on the strength of the selection and the effective population size, which is the number of individuals capable of breeding.[105] Natural selection usually predominates in large populations, whereas genetic drift dominates in small populations. The dominance of genetic drift in small populations can even lead to the fixation of slightly deleterious mutations.[106] As a result, changing population size can dramatically influence the course of evolution. Population bottlenecks, where the population shrinks temporarily and therefore loses genetic variation, result in a more uniform population.[43]
Natural selection

Natural selection is the process by which genetic mutations that enhance reproduction become, and remain, more common in successive generations of a population. It has often been called a "self-evident" mechanism because it necessarily follows from three simple facts:

* Heritable variation exists within populations of organisms.
* Organisms produce more offspring than can survive.
* These offspring vary in their ability to survive and reproduce.

These conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors pass these advantageous traits on, while traits that do not confer an advantage are not passed on to the next generation.[107]

The central concept of natural selection is the evolutionary fitness of an organism.[108] Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.[108] 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.[109] 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.[108]

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".[110] 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.[1] 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 (see Dollo's law).[111][112]
A chart showing three types of selection. 1.Disruptive selection 2.Stabilizing selection 3.Directional selection

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.[113] 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 stabilizing selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity.[107][114] This would, for example, cause organisms to slowly become all the same height.

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.[115] Traits that evolved through sexual selection are particularly prominent in males of some animal species, despite traits such as cumbersome antlers, mating calls or bright colours that attract predators, decreasing the survival of individual males.[116] This survival disadvantage is balanced by higher reproductive success in males that show these hard to fake, sexually selected traits.[117]

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 (ie: exchange of materials between living and nonliving parts) within the system."[118] 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.

An active area of research is the unit of selection, with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and species.[119][120] None of these are mutually exclusive and selection can act on multiple levels simultaneously.[121] An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome.[122] Selection at a level above the individual, such as group selection, may allow the evolution of co-operation, as discussed below.[123]
Genetic drift

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in offspring are a random sample of those in the parents, as well as from the role that chance plays in determining whether a given individual will survive and reproduce. In mathematical terms, alleles are subject to sampling error. As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward randomly (in a random walk). This drift halts when an allele eventually becomes fixed, either by disappearing from the population, or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.[124]

The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.[125] The precise measure of population that is important is called the effective population size. The effective population is always smaller than the total population since it takes into account factors such as the level of inbreeding, the number of animals that are too old or young to breed, and the lower probability of animals that live far apart managing to mate with each other.[126]

An example when genetic drift is probably of central importance in determining a trait is the loss of pigments from animals that live in caves, a change that produces no obvious advantage or disadvantage in complete darkness.[127] However, it is usually difficult to measure the relative importance of selection and drift,[128] so the comparative importance of these two forces in driving evolutionary change is an area of current research.[129] These investigations were prompted by the neutral theory of molecular evolution, which proposed that most evolutionary changes are the result of the fixation of neutral mutations that do not have any immediate effects on the fitness of an organism.[130] Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.[131] This form of the neutral theory is now largely abandoned, since it does not seem to fit the genetic variation seen in nature.[132][133] However, a more recent and better-supported version of this model is the nearly neutral theory, where most mutations only have small effects on fitness.[107]
Outcomes

Evolution influences every aspect of the form and behaviour of organisms. Most prominent are the specific behavioral 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 co-operating 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[citation needed].

These outcomes of evolution are sometimes divided into macroevolution, which is evolution that occurs at or above the level of species, such as extinction and speciation, and microevolution, which is smaller evolutionary changes, such as adaptations, within a species or population.[134] In general, macroevolution is regarded as the outcome of long periods of microevolution.[135] Thus, the distinction between micro- and macroevolution is not a fundamental one – the difference is simply the time involved.[136] 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.[137][138][139]

A common misconception is that evolution has goals or long-term plans; realistically however, evolution has no long-term goal and does not necessarily produce greater complexity.[140][141] 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.[142] For example, the overwhelming majority of species are microscopic prokaryotes, which form about half the world's biomass despite their small size,[143] and constitute the vast majority of Earth's biodiversity.[144] 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.[145] Indeed, the evolution of microorganisms is particularly important to modern evolutionary research, since their rapid reproduction allows the study of experimental evolution and the observation of evolution and adaptation in real time.[146][147]
Adaptation

Adaptation is one of the basic phenomena of biology,[148] and is the process whereby an organism becomes better suited to its habitat.[149][150] 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, or the ability of horses to run fast and escape predators. 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.[151] 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.[152]
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.[153]
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.[154]

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.[155] Other striking examples are the bacteria Escherichia coli evolving the ability to use citric acid as a nutrient in a long-term laboratory experiment,[156] Flavobacterium evolving a novel enzyme that allows these bacteria to grow on the by-products of nylon manufacturing,[157][158] and the soil bacterium Sphingobium evolving an entirely new metabolic pathway that degrades the synthetic pesticide pentachlorophenol.[159][160] 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).[161][162]
A baleen whale skeleton, a and b label flipper bones, which were adapted from front leg bones: while c indicates vestigial leg bones, suggesting an adaptation from land to sea.[163]

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.[164] However, since all living organisms are related to some extent,[165] 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.[166][167]

During adaptation, some structures may lose their original function and become vestigial structures.[168] 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,[169] the non-functional remains of eyes in blind cave-dwelling fish,[170] wings in flightless birds,[171] and the presence of hip bones in whales and snakes.[163] Examples of vestigial structures in humans include wisdom teeth,[172] the coccyx,[168] the vermiform appendix,[168] and other behavioral vestiges such as goose bumps,[173] and primitive reflexes.[174][175][176][177]

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.[178] 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.[178] Within cells, molecular machines such as the bacterial flagella[179] and protein sorting machinery[180] evolved by the recruitment of several pre-existing proteins that previously had different functions.[134] 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.[181][182]

A critical principle of ecology is that of competitive exclusion: no two species can occupy the same niche in the same environment for a long time.[183] Consequently, natural selection will tend to force species to adapt to different ecological niches. This may mean that, for example, two species of cichlid fish adapt to live in different habitats, which will minimise the competition between them for food.[184]

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations and exaptations.[185] This research addresses the origin and evolution of embryonic development and how modifications of development and developmental processes produce novel features.[186] These studies have shown that evolution can alter development to create new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the middle ear in mammals.[187] 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.[188] It is now becoming clear that most alterations in the form of organisms are due to changes in a small set of conserved genes.[189]
Co-evolution

Interactions between organisms can produce both conflict and co-operation. 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 co-evolution.[190] 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.[191]
Co-operation

However, not all interactions between species involve conflict.[192] 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.[193] 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.[194]

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.[47]

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.[195] 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.[196] Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.[197Speciation

Speciation is the process where a species diverges into two or more descendant species.[198] Darwinian theory involves a shift away from viewing species as static ideal types, defined by the presence of a particular trait, to viewing them as populations with a history that requires more of a statistical approach for the analysis of multiple variable traits.[199][200][201] This view is counterintuitive since the classical idea of species is still widely held, with a species seen as a class of organisms exemplified by a "type specimen" that bears all the traits common to this species. Instead, a species is now defined as a separately evolving lineage that forms a single gene pool. Although properties such as genetics and morphology are used to help separate closely related lineages, this definition has fuzzy boundaries.[202] Indeed, the exact definition of the term "species" is still controversial, particularly in prokaryotes,[203] and this is called the species problem.[204] Biologists have proposed a range of more precise definitions, but the definition used is a pragmatic choice that depends on the particularities of the species concerned.[204] Typically the actual focus on biological study is the population, an observable interacting group of organisms, rather than a species, an observable similar group of individuals.

Speciation has been observed multiple times under both controlled laboratory conditions and in nature.[205] In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four mechanisms for 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.[206][207] As selection and drift act independently on populations isolated from the rest of their species, separation may eventually produce organisms that cannot interbreed.[208]

The second mechanism 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 through both rapid genetic drift and selection on a small gene pool.[209]

The third mechanism of speciation 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.[198] 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.[210] 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.[211]
Geographical isolation of finches on the Galápagos Islands produced over a dozen new species.

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.[212] Generally, sympatric speciation in animals requires the evolution of both genetic differences and non-random mating, to allow reproductive isolation to evolve.[213]

One type of sympatric speciation involves cross-breeding 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.[214] 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.[215] An example of such a speciation event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa cross-bred to give the new species Arabidopsis suecica.[216] This happened about 20,000 years ago,[217] and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process.[218] 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.[95]

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.[219] 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.[220]
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.[221] Nearly all animal and plant species that have lived on Earth are now extinct,[222] and extinction appears to be the ultimate fate of all species.[223] These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events.[224] The Cretaceous–Tertiary extinction event, during which the non-avian dinosaurs went extinct, is the most well-known, but the earlier Permian–Triassic extinction event was even more severe, with approximately 96 percent of species driven to extinction.[224] 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 percent of species may be extinct by the mid 21st century.[225] Human activities are now the primary cause of the ongoing extinction event;[226] global warming may further accelerate it in the future.[227]

The role of extinction in evolution is not very well understood and may depend on which type of extinction is considered.[224] 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 (competitive exclusion).[19] 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.[119] 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.[228]
Evolutionary history of life
Origin of life

The origin of life is a necessary precursor for biological evolution, but understanding that evolution occurred once organisms appeared and investigating how this happens does not depend on understanding exactly how life began.[229] The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions, but it is unclear how this occurred.[230] Not much is certain about the earliest developments in life, the structure of the first living things, or the identity and nature of any last universal common ancestor or ancestral gene pool.[231][232] Consequently, there is no scientific consensus on how life began, but proposals include self-replicating molecules such as RNA,[233] and the assembly of simple cells.[234]
Common descent

All organisms on Earth are descended from a common ancestor or ancestral gene pool.[165][235] Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events.[236] The common descent of organisms was first deduced from four simple facts about organisms: First, they have geographic distributions that cannot be explained by local adaptation. Second, the diversity of life is not a set of completely unique organisms, but organisms that share morphological similarities. Third, vestigial traits with no clear purpose resemble functional ancestral traits, and finally, that organisms can be classified using these similarities into a hierarchy of nested groups – similar to a family tree.[14] However, modern research has suggested that, due to horizontal gene transfer, this "tree of life" may be more complicated than a simple branching tree since some genes have spread independently between distantly related species.[237][238]

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.[239] By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry.

More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and amino acids.[240] 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.[241] For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 96% of their genomes and analyzing the few areas where they differ helps shed light on when the common ancestor of these species existed.[242]
Evolution of life

Despite the uncertainty on how life began, it is generally accepted that prokaryotes inhabited the Earth from approximately 3–4 billion years ago.[244][245] No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years.[246]

The eukaryotes were the next major change in cell structure. These came from ancient bacteria being engulfed by the ancestors of eukaryotic cells, in a cooperative association called endosymbiosis.[104][247] The engulfed bacteria and the host cell then underwent co-evolution, with the bacteria evolving into either mitochondria or hydrogenosomes.[248] An independent second engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.[249] It is unknown when the first eukaryotic cells appeared though they first emerged between 1.6 – 2.7 billion years ago.

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.[244][250] The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria.[251]

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.[252] Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.[253]

About 500 million years ago, plants and fungi colonised the land, and were soon followed by arthropods and other animals.[254] Insects were particularly successful and even today make up the majority of animal species.[255] Amphibians first appeared around 300 million years ago, followed by early amniotes, then mammals around 200 million years ago and birds around 100 million years ago (both from "reptile"-like lineages). 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.[144]
Applications

Evolutionary biology, and in particular the understanding of how organisms evolve through natural selection, is an area of science with many practical applications.[256] A major technological application of evolution is artificial selection, which is the intentional selection of certain traits in a population of organisms. Humans have used artificial selection for thousands of years in the domestication of plants and animals.[257] More recently, such selection has become a vital part of genetic engineering, with selectable markers such as antibiotic resistance genes being used to manipulate DNA in molecular biology. It is also possible to use repeated rounds of mutation and selection to evolve proteins with particular properties, such as modified enzymes or new antibodies, in a process called directed evolution.[258]

Understanding the changes that have occurred during organism's evolution can reveal the genes needed to construct parts of the body, genes which may be involved in human genetic disorders.[259] 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.[260] This helped identify genes required for vision and pigmentation, such as crystallins and the melanocortin 1 receptor.[261] Similarly, comparing the genome of the Antarctic icefish, which lacks red blood cells, to close relatives such as the Antarctic rockcod revealed genes needed to make these blood cells.[262]

As evolution can produce highly optimised processes and networks, it has many applications in computer science. Here, simulations of evolution using evolutionary algorithms and artificial life started with the work of Nils Aall Barricelli in the 1960s, and was extended by Alex Fraser, who published a series of papers on simulation of artificial selection.[263] Artificial evolution became a widely recognised optimisation method as a result of the work of Ingo Rechenberg in the 1960s and early 1970s, who used evolution strategies to solve complex engineering problems.[264] Genetic algorithms in particular became popular through the writing of John Holland.[265] As academic interest grew, dramatic increases in the power of computers allowed practical applications, including the automatic evolution of computer programs.[266] 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.[267]
Social and cultural responses

n 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 centered on the philosophical, social and religious implications of evolution. Nowadays, the fact that organisms evolve is uncontested in the scientific literature and the modern evolutionary synthesis is widely accepted by scientists.[19] However, evolution remains a contentious concept for some theists.[269]

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 respective religions and who raise various objections to evolution.[134][270][271] 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 human mental and moral faculties, which had been thought purely spiritual, are not distinctly separated from those of other animals.[13] In some countries—notably the United States—these tensions between science and religion have fueled the current creation-evolution controversy, a religious conflict focusing on politics and public education.[272] While other scientific fields such as cosmology[273] and Earth science[274] 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 about a generation later and 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 the form of intelligent design, to be excluded once again in the 2005 Kitzmiller v. Dover Area School District case.[275]

Another example somewhat associated with evolutionary theory that is now widely regarded as unwarranted is "Social Darwinism", a derogatory term associated with the 19th century Malthusian theory developed by Whig philosopher Herbert Spencer. It was later expanded by others into ideas about "survival of the fittest" in commerce and human societies as a whole, and led to claims that social inequality, sexism, racism, and imperialism were justified.[276] However, these ideas contradict Darwin's own views, and contemporary scientists and philosophers consider these ideas to be neither mandated by evolutionary theory nor supported by data.[277][278][279]
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Ecology

Ecology (from Greek: οἶκος, "house"; -λογία, "study of") is the scientific study of the relation of living organisms to each other and their surroundings. Ecosystems are defined by a web, community, or network of individuals that arrange into a self-organized and complex hierarchy of pattern and process. Ecosystems create a biophysical feedback between living (biotic) and nonliving (abiotic) components of an environment that generates and regulates the biogeochemical cycles of the planet. Ecosystems provide goods and services that sustain human societies and general well-being. Ecosystems are sustained by biodiversity within them.[1][2] Biodiversity is the full-scale of life and its processes, including genes, species and ecosystems forming lineages that integrate into a complex and regenerative spatial arrangement of types, forms, and interactions.[3]

Ecology is a sub-discipline of biology, the study of life. The word "ecology" ("oekologie") was coined in 1866 by the German scientist Ernst Haeckel (1834–1919). Haeckel was a zoologist, artist, writer, and later in life a professor of comparative anatomy.[4][5] Ancient philosophers of Greece, including Hippocrates and Aristotle, were among the earliest to record notes and observations on the natural history of plants and animals; the early rudiments of modern ecology. Modern ecology mostly branched out of natural history science that flourished in the late 19th century. Charles Darwin's evolutionary treatise and the concept of adaptation as it was introduced in 1859 is a pivotal cornerstone in modern ecological theory.[1][2][6]

Ecology is not synonymous with environment, environmentalism, natural history or environmental science.[1][7] Ecology is closely related to the biological disciplines of physiology, evolution, genetics and behavior.[8][9] An understanding of how biodiversity affects ecological function is an important focus area in ecological studies. Ecosystems sustain every life-supporting function on the planet, including climate regulation, water filtration, soil formation (pedogenesis), food, fibe
r

s, medicines, erosion control, and many other natural features of historical, spiritual or scientific value.[10][11]

Ecologists seek to explain:

* life processes and adaptations
* distribution and abundance of organisms
* the movement of materials and energy through living communities
* the successional development of ecosystems,[8] and
* the abundance and distribution of biodiversity in context of the environment.[1][7][8]

There are many practical applications of ecology in conservation biology, wetland management, natural resource management (agriculture, forestry, fisheries), city planning (urban ecology), community health, economics, basic & applied science and it provides a conceptual framework for understanding and researching human social interaction (human ecology).[8][12][13][14]
Scale and complexity

Ecosystems are forever confronted with a range of natural environmental fluctuations that vary transiently in magnitude through space and time.[16] It can take thousands of years for ecological processes to mature; the life-span of a tree, for example, can encompass different successional stages. The ecological process is extended even further through time as trees die, decay and provide habitat as nurse logs or coarse woody debris. The area of an ecosystem can vary greatly from tiny to vast. A single tree is of little consequence to the classification of a forest ecosystem, but critically relevant to the smaller organisms living in and on it.[17] Several generations of an aphid population can exist over the lifespan of a single leaf. Each of those aphids, in turn, support diverse bacterial communities.[18] Fine scale structure of aphid populations can be constrained by top-down influences of tree growth that is related to site specific variables, such as soil type, moisture content, slope of the land, and forest canopy closure. Likewise, finer scale dynamics operating in the aphid populations can impart bottom-up influence on tree growth rates.[19] The scale of ecological dynamics can operate as a closed island with respect to local site variables, such as aphids migrating on a tree, while at the same time remain open with regard to broader scale influences, such as atmosphere or climate. Hence, ecologists have devised means of hierarchically classifying ecosystems by analyzing data collected from finer scale units, such as vegetation associations, climate, and soil types, and integrate this information to identify larger emergent patterns of uniform organization and processes that operate on regional, local, and chronological scales.[20][21]

There are different views on complexity and how it relates to ecology. One perspective lumps things that we do not understand into this category by virtue of the computational effort it would require to piece together the numerous interacting parts. Alternatively, complexity in life sciences can be viewed as emergent self-organized systems with multiple possible outcomes directed by random accidents of history; an extension of the first perspective.[22] Global patterns of biological diversity are complex. This biocomplexity stems from the interplay among ecological processes that operate and influence patterns that grade into each other, such as transitional areas or ecotones that stretch across different scales.[23] "Complexity in ecology is of at least six distinct types: spatial, temporal, structural, process, behavioral, and geometric."[24]:3 Small scale patterns do not necessarily explain large scale phenomena, otherwise captured in the expression 'the sum is greater than the parts'.[25][26] Ecologists have identified emergent and self-organizing phenomena that operate at different environmental scales of influence, ranging from molecular to planetary, and these require different sets of scientific explanation.[27][28] Long-term ecological studies provide important track records to better understand the complexity of ecosystems over longer temporal and broader spatial scales. The International Long Term Ecological Network[29] manages and exchanges scientific information among research sites. The longest experiment in existence is the Park Grass Experiment that was initiated in 1856.[30] Another example includes the Hubbard Brook study in operation since 1960.[31]

To structure the study of ecology into a manageable framework of understanding, the biological world is conceptually organized as a nested hierarchy of organization, ranging in scale from genes, to cells, to tissues, to organs, to organisms, to species and up to the level of the biosphere.[32] Together these hierarchical scales of life form a panarchy.[22] Ecosystems are primarily researched at three key levels of organization—organisms, populations, and communities. Ecologists study ecosystems by sampling a certain number of individuals that are representative of a population. Ecosystems consist of communities interacting with each other and the environment. In ecology, communities are created by the interaction of the populations of different species in an area.[1][33]

Biodiversity is the variety of life and its processes. It includes the variety of living organisms, the genetic differences among them, the communities and ecosystems in which they occur, and the ecological and evolutionary processes that keep them functioning, yet ever changing and adapting.[34]:5

Biodiversity (an abbreviation of biological diversity) describes the diversity of life from genes to ecosystems and spans every level of biological organization. Biodiversity means different things to different people and there are many ways to index, measure, characterize, and represent its complex organization.[3][35] Biodiversity includes species diversity, ecosystem diversity, genetic diversity and the complex processes operating at and among these respective levels.[35][36][37] Biodiversity plays an important role in ecological health as much as it does for human health.[38][39] Preventing or prioritizing species extinctions is one way to preserve biodiversity, but populations, the genetic diversity within them and ecological processes, such as migration, are being threatened on global scales and disappearing rapidly as well. Conservation priorities and management techniques require different approaches and considerations to address the full ecological scope of biodiversity. Populations and species migration, for example, are more sensitive indicators of ecosystem services that sustain and contribute natural capital toward the well-being of humanity.[40][41][42][43] An understanding of biodiversity has practical application for ecosystem-based conservation planners as they make ecologically responsible decisions in management recommendations to consultant firms, governments and industry.[44]
Ecological niche and habitat
There are many definitions of the niche dating back to 1917,[47] but G. Evelyn Hutchinson made conceptual advances in 1957[48][49] and introduced the most widely accepted definition: "The niche is the set of biotic and abiotic conditions in which a species is able to persist and maintain stable population sizes."[47]:519 The ecological niche is a central concept in the ecology of organisms and is sub-divided into the fundamental and the realized niche. The fundamental niche is the set of environmental conditions under which a species is able to persist. The realized niche is the set of environmental plus ecological conditions under which a species persists.[1][47][49] The Hutchisonian niche is defined more technically as an "euclidean hyperspace whose dimensions are defined as environmental variables and whose size is a function of the number of values that the environmental values may assume for which an organism has positive fitness."[50]:71

The habitat of a species is a related but distinct concept that describes the environment over which a species is known to occur and the type of community that is formed as a result.[51] More specifically, "habitats can be defined as regions in environmental space that are composed of multiple dimensions, each representing a biotic or abiotic environmental variable; that is, any component or characteristic of the environment related directly (e.g. forage biomass and quality) or indirectly (e.g. elevation) to the use of a location by the animal."[52]:745 For example, the habitat might refer to an aquatic or terrestrial environment that can be further categorized as montane or alpine ecosystems.

Biogeographical patterns and range distributions are explained or predicted through knowledge and understanding of a species traits and niche requirements.[53] Species have functional traits that are uniquely adapted to the ecological niche. A trait is a measurable property, phenotype, or characteristic of an organism that influences its performance. Genes play an important role in the development and expression of traits.[54] Resident species evolve traits that are fitted to their local environment. This tends to afford them a competitive advantage and discourages similarly adapted species from having an overlapping geographic range. The competitive exclusion principle suggests that two species cannot coexist indefinitely by living off the same limiting resource. When similarly adapted species are found to overlap geographically, closer inspection reveals subtle ecological differences in their habitat or dietary requirements.[55]
Niche construction

Organisms are subject to environmental pressures, but they are also modifiers of their habitats. The regulatory feedback between organisms and their environment can modify conditions from local (e.g., a beaver pond) to global scales (e.g., Gaia), over time and even after death, such as decaying logs or silica skeleton deposits from marine organisms.[57] The process and concept of ecosystem engineering has also been called niche construction. Ecosystem engineers are defined as: "...organisms that directly or indirectly modulate the availability of resources to other species, by causing physical state changes in biotic or abiotic materials. In so doing they modify, maintain and create habitats."[58]:373

The ecosystem engineering concept has stimulated a new appreciation for the degree of influence that organisms have on the ecosystem and evolutionary process. The terms niche construction are more often used in reference to the under appreciated feedback mechanism of natural selection imparting forces on the abiotic niche.[45][59] An example of natural selection through ecosystem engineering occurs in the nests of social insects, including ants, bees, wasps, and termites. There is an emergent homeostasis or homeorhesis in the structure of the nest that regulates, maintains and defends the physiology of the entire colony. Termite mounds, for example, maintain
a constant internal temperature through the design of air-conditioning chimneys. The structure of the nests themselves are subject to the forces of natural selection. Moreover, the nest can survive over successive generations, which means that ancestors inherit both genetic material and a legacy niche that was constructed before their time.[2][45][46][60]
Population ecology

The population is the unit of analysis in population ecology. A population consists of individuals of the same species that live, interact and migrate through the same niche and habitat.[61] A primary law of population ecology is the Malthusian growth model.[62] This law states that:

"...a population will grow (or decline) exponentially as long as the environment experienced by all individuals in the population remains constant."[62]:18

This Malthusian premise provides the basis for formulating predictive theories and tests that follow. Simplified population models usually start with four variables including death, birth, immigration, and emigration. Mathematical models are used to calculate changes in population demographics using a null model. A null model is used as a null hypothesis for statistical testing. The null hypothesis states that random processes create observed patterns. Alternatively the patterns differ significantly from the random model and require further explanation. Models can be mathematically complex where "...several competing hypotheses are simultaneously confronted with the data."[63] An example of an introductory population model describes a closed population, such as on an island, where immigration and emigration does not take place. In these island models the rate of population change is described by:

\frac{dN}{dT} = B - D = bN - dN = (b - d)N = rN,

where N is the total number of individuals in the population, B is the number of births, D is the number of deaths, b and d are the per capita rates of birth and death respectively, and r is the per capita rate of population change. This formula can be read out as the rate of change in the population (dN/dT) is equal to births minus deaths (B – D).[62][64]

Using these modelling techniques, Malthus' population principle of growth was later transformed into a model known as the logistic equation:

\frac{dN}{dT} = aN(1-\frac{N}{K}),

where N is the number of individuals measured as biomass density, a is the maximum per-capita rate of change, and K is the carrying capacity of the population. The formula can be read as follows: the rate of change in the population (dN/dT) is equal to growth (aN) that is limited by carrying capacity (1 – N/K). The discipline of population ecology builds upon these introductory models to further understand demographic processes in real study populations and conduct statistical tests. The field of population ecology often uses data on life history and matrix algebra to develop projection matrices on fecundity and survivorship. This information is used for managing wildlife stocks and setting harvest quotas.[64][65]
Metapopulation ecology

Populations are also studied and modeled according to the metapopulation concept. The metapopulation concept was introduced in 1969:[67] "as a population of populations which go extinct locally and recolonize."[68]:105 Metapopulation ecology is another statistical approach that is often used in conservation research.[69] Metapopulation research simplifies the landscape into patches of varying levels of quality.[70]

In metapopulation terminology there are emigrants (individuals that leave a patch), immigrants (individuals that move into a patch) and sites are classed either as sources or sinks. A site is a generic term that refers to places where ecologists sample populations, such as ponds or defined sampling areas in a forest. Source patches are productive sites that generate a seasonal supply of juveniles that migrate to other patch locations. Sink patches are unproductive sites that only receive migrants and will go extinct unless rescued by an adjacent source patch or environmental conditions become more favorable. Metapopulation models examine patch dynamics over time to answer questions about spatial and demographic ecology. The ecology of metapopulations is a dynamic process of extinction and colonization. Small patches of lower quality (i.e., sinks) are maintained or rescued by a seasonal influx of new immigrants. A dynamic metapopulation structure evolves from year to year, where some patches are sinks in dry years and become sources when conditions are more favorable. Ecologists use a mixture of computer models and field studies to
explain metapopulation structure.[71][72]
Community ecology
Community ecology is the study of the interactions among a collection of interdependent species that cohabitate the same geographic area. An example of a study in community ecology might measure primary production in a wetland in relation to decomposition and consumption rates. This requires an understanding of the community connections between plants (i.e., primary producers) and the decomposers (e.g., fungi and bacteria).[74] or the analysis of predator-prey dynamics affecting amphibian biomass.[75] Food webs and trophic levels are two widely employed conceptual models used to explain the linkages among species.[76][77]
Food webs

A food web is the archetypal ecological network. They are a type of concept map that illustrate pathways of energy flows in an ecological community, usually starting with solar energy being used by plants during photosynthesis. As plants grow, they accumulate carbohydrates and are eaten by grazing herbivores. Step by step lines or relations are drawn until a web of life is illustrated.[78][79][80][81]
Freshwater aquatic and terrestrial food-webs
Generalized food web of waterbirds from Chesapeake Bay

There are different ecological dimensions that can be mapped to create more complicated food webs, including: species composition (type of species), richness (number of species), biomass (the dry weight of plants and animals), productivity (rates of conversion of energy and nutrients into growth), and stability (food webs over time). A food web diagram illustrating species composition shows how change in a single species can directly and indirectly influence many others. Microcosm studies are used to simplify food web research into semi-isolated units such as small springs, decaying logs, and laboratory experiments using organisms that reproduce quickly, such as daphnia feeding on algae grown under controlled environments in jars of water.[82][83]

Principles gleaned from food web microcosm studies are used to extrapolate smaller dynamic concepts to larger systems.[83] Food webs are limited because they are generally restricted to a specific habitat, such as a cave or a pond. The food web illustration (right) only shows a small part of the complexity connecting the aquatic system to the adjacent terrestrial land. Many of these species migrate into other habitats to distribute their effects on a larger scale. In other words, food webs are incomplete, but are nonetheless a valuable tool in understanding community ecosystems.[84]
Trophic dynamics

The Greek root of the word troph, τροφή, trophē, means food or feeding. Links in food-webs primarily connect feeding relations or trophism among species. Biodiversity within ecosystems can be organized into vertical and horizontal dimensions. The vertical dimension represents feeding relations that become further removed from the base of the food chain up toward top predators. The horizontal dimension represents the abundance or biomass at each level.[85] When the relative abundance or biomass of each functional feeding group is stacked into their respective trophic levels they naturally sort into a ‘pyramid of numbers’.[86] Functional groups are broadly categorized as autotrophs (or primary producers), heterotrophs (or consumers), and detrivores (or decomposers). Heterotrophs can be further sub-divided into different functional groups, including: primary consumers (strict herbivores), secondary consumers (predators that feed exclusively on herbivores) and tertiary consumers (predators that feed on a mix of herbivores and predators).[87] Omnivores do not fit neatly into a functional category because they eat both plant and animal tissues. It has been suggested that omnivores have a greater functional influence as predators because relative to herbivores they are comparatively inefficient at grazing.[88]

The decomposition of dead organic matter, such as leaves falling on the forest floor, turns into soils that feed plant production. The total sum of the planet's soil ecosystems is called the pedosphere where a very large proportion of the Earth's biodiversity sorts into other trophic levels. Invertebrates that feed and shred larger leaves, for example, create smaller bits for smaller organisms in the feeding chain. Collectively, these are the detrivores that regulate soil formation.[89][90] Tree roots, fungi, bacteria, worms, ants, beetles, centipedes, spiders, mammals, birds, reptiles, amphibians and other less familiar creatures all work to create the trophic web of life in soil ecosystems. As organisms feed and migrate through soils they physically displace materials, which is an important ecological process called bioturbation. Biomass of soil microorganisms are influenced by and feed back into the trophic dynamics of the exposed solar surface ecology. Paleoecological studies of soils places the origin for bioturbation to a time before the Cambrian period. Other events, such as the evolution of trees and amphibians moving into land in the Devonian period played a significant role in the development of soils and ecological trophism.[75][90][91]
Functional trophic groups sort out hierarchically into pyramidic trophic levels because it requires specialized adaptations to become a photosynthesizer or a predator, so few organisms have the adaptations needed to combine both abilities. This explains why functional adaptations to trophism (feeding) organizes different species into emergent functional groups.[88] Trophic levels are part of the holistic or complex systems view of ecosystems.[92][93] Each trophic level contains unrelated species that grouped together because they share common ecological functions. Grouping functionally similar species into a trophic system gives a macroscopic image of the larger functional design.[94]
Keystone species

A keystone species is a species that is disproportionately connected to more species in the food-web. Keystone species have lower levels of biomass in the trophic pyramid relative to the importance of their role. The many connections that a keystone species holds means that it maintains the organization and structure of entire communities. The loss of a keystone species results in a range of dramatic cascading effects that alters trophic dynamics, other food-web connections and can cause the extinction of other species in the community.[95][96]

Sea otters (Enhydra lutris) are commonly cited as an example of a keystone species because they limit the density of sea urchins that feed on kelp. If sea otters are removed from the system, the urchins graze until the kelp beds disappear and this has a dramatic effect on community structure.[97] Hunting of sea otters, for example, is thought to have indirectly led to the extinction of the Steller's Sea Cow (Hydrodamalis gigas).[98] While the keystone species concept has been used extensively as a conservation tool, it has been criticized for being poorly defined from an operational stance. It is very difficult to experimentally determine in each different ecosystem what species may hold a keystone role. Furthermore, food-web theory suggests that keystone species may not be all that common. It is therefore unclear how generally the keystone species model can be applied.[97][99]
Ecosystem ecology
The concept of the ecosystem was first introduced in 1935 to describe habitats within biomes that form an integrated whole and a dynamically responsive system having both physical and biological complexes. Within an ecosystem there are inseparable ties that link organisms to the physical and biological components of their environment to which they are adapted.[100] Ecosystems are complex adaptive systems where the interaction of life processes form self-organizing patterns across different scales of time and space.[101] This section introduces key areas of ecosystem ecology that are used to inquire, understand and explain observed patterns of biodiversity and ecosystem function across different scales of organization.
Biome
Ecological units of organization are defined through reference to any magnitude of space and time on the planet. Communities of organisms, for example, are somewhat arbitrarily defined, but the processes of life integrate at different levels and organize into more complex wholes. Biomes, for example, are a larger unit of organization that categorize regions of the Earth's ecosystems mainly according to the structure and composition of vegetation.[102] Different researchers have applied different methods to define continental boundaries of biomes dominated by different functional types of vegetative communities that are limited in distribution by climate, precipitation, weather and other environmental variables. Examples of biome names include: tropical rainforest, temperate broadleaf and mixed forests, temperate deciduous forest, taiga, tundra, hot desert, and polar desert.[103] Other researchers have recently started to categorize other types of biomes, such as the human and oceanic microbiomes. To a microbe, the human body is a habitat and a landscape.[104] The microbiome has been largely discovered through advances in molecular genetics that have revealed a hidden richness of microbial diversity on the planet. The oceanic microbiome plays a significant role in the ecological biogeochemistry of the planet's oceans.[105]
Biosphere
Ecological theory has been used to explain self-emergent regulatory phenomena at the planetary scale. The largest scale of ecological organization is the biosphere: the total sum of ecosystems on the planet. Ecological relations regulate the flux of energy, nutrients, and climate all the way up to the planetary scale. For example, the dynamic history of the planetary CO2 and O2 composition of the atmosphere has been largely determined by the biogenic flux of gases coming from respiration and photosynthesis, with levels fluctuating over time and in relation to the ecology and evolution of plants and animals.[106] When sub-component parts are organized into a whole there are oftentimes emergent properties that describe the nature of the system. This the Gaia hypothesis,[28] and is an example of holism applied in ecological theory.[107] The ecology of the planet acts as a single regulatory or holistic unit called Gaia. The Gaia hypothesis states that there is an emergent feedback loop generated by the metabolism of living organisms that maintains the temperature of the Earth and atmospheric conditions within a narrow self-regulating range of tolerance.[28]
Relation to evolution
Ecology and evolution are considered sister disciplines of the life sciences. Natural selection, life history, development, adaptation, populations, and inheritance are examples of concepts that thread equally into ecological and evolutionary theory. Morphological, behavioral and/or genetic traits, for example, can be mapped onto evolutionary trees to study the historical development of a species in relation to their functions and roles in different ecological circumstances. In this framework, the analytical tools of ecologists and evolutionists overlap as they organize, classify and investigate life through common systematic principals, such as phylogenetics or the Linnaean system of taxonomy.[108] The two disciplines often appear together, such as in the title of the journal Trends in Ecology and Evolution.[109] There is no sharp boundary separating ecology from evolution and they differ more in their areas of applied focus. Both disciplines discover and explain emergent and unique properties and processes operating across different spatial or temporal scales of organization.[28][110][111] While the boundary between ecology and evolution is not always clear, it is understood that ecologists study the abiotic and biotic factors that influence the evolutionary process.[7][112]
Behavioral ecology

All organisms are motile to some extent. Even plants express complex behavior, including memory and communication.[114] Behavioral ecology is the study of ethology and its ecological and evolutionary implications. Ethology is the study of observable movement or behavior in nature. This could include investigations of motile sperm of plants, mobile phytoplankton, zooplankton swimming toward the female egg, the cultivation of fungi by weevils, the mating dance of a salamander, or social gatherings of amoeba.[115][116][117][118][119]

Adaptation is the central unifying concept in behavioral ecology."International Society for Behavioral Ecology". http://www.behavecol.com/pages/society/welcome.html. Behaviors can be recorded as traits and inherited in much the same way that eye and hair color can. Behaviors evolve and become adapted to the ecosystem because they are subject to the forces of natural selection.[36] Hence, behaviors can be adaptive, meaning that they evolve functional utilities that increases reproductive success for the individuals that inherit such traits.[120] This is also the technical definition for fitness in biology, which is a measure of reproductive success over successive generations.[36]

Predator-prey interactions are an introductory concept into food-web studies as well as behavioral ecology.[121] Prey species can exhibit different kinds of behavioral adaptations to predators, such as avoid, flee or defend. Many prey species are faced with multiple predators that differ in the degree of danger posed. To be adapted to their environment and face predatory threats, organisms must balance their energy budgets as they invest in different aspects of their life history, such as growth, feeding, mating, socializing, or modifying their habitat. Hypotheses posited in behavioral ecology are generally based on adaptive principals of conservation, optimization or efficiency.[1][7][122] For example,

"The threat-sensitive predator avoidance hypothesis predicts that prey should assess the degree of threat posed by different predators and match their behavior according to current levels of risk."[123]

"The optimal flight initiation distance occurs where expected postencounter fitness is maximized, which depends on the prey’s initial fitness, benefits obtainable by not fleeing, energetic escape costs, and expected fitness loss due to predation risk."[124]
Symbiosis: Leafhoppers (Eurymela fenestrata) are protected by ants (Iridomyrmex purpureus) in a symbiotic relationship. The ants protect the leafhoppers from predators and in return the leafhoppers feeding on plants exude honeydew from their anus that provides energy and nutrients to tending ants.[125]

Elaborate sexual displays and posturing are encountered in the behavioral ecology of animals. The birds of paradise, for example, display elaborate ornaments and song during courtship. These displays serve a dual purpose of signaling healthy or well-adapted individuals and desirable genes. The elaborate displays are driven by sexual selection as an advertisement of quality of traits among male suitors.[126]Social ecology
Social ecological behaviors are notable in the social insects, slime moulds, social spiders, human society, and naked mole rats where eusocialism has evolved. Social behaviors include reciprocally beneficial behaviors among kin and nest mates.[36][117][127] Social behaviors evolve from kin and group selection. Kin selection explains altruism through genetic relationships, whereby an altruistic behavior leading to death is rewarded by the survival of genetic copies distributed among surviving relatives. The social insects, including ants, bees and wasps are most famously studied for this type of relationship because the male drones are clones that share the same genetic make-up as every other male in the colony.[36] In contrast, group selectionists find examples of altruism among non-genetic relatives and explain this through selection acting on the group, whereby it becomes selectively advantageous for groups if their members express altruistic behaviors to one another. Groups that are predominantly altruists beat groups that are predominantly selfish.[36][128]
Coevolution

Ecological interactions can be divided into host and associate relationships. A host is any entity that harbors another that is called the associate.[129] Host and associate relationships among species that are mutually or reciprocally beneficial are called mutualisms. If the host and associate are physically connected, the relationship is called symbiosis. Approximately 60% of all plants, for example, have a symbiotic relationship with arbuscular mycorrhizal fungi. Symbiotic plants and fungi exchange carbohydrates for mineral nutrients.[130] Symbiosis differs from indirect mutualisms where the organisms live apart. For example, tropical rainforests regulate the Earth's atmosphere. Trees living in the equatorial regions of the planet supply oxygen into the atmosphere that sustains species living in distant polar regions of the planet. This relationship is called commensalism because many other host species receive the benefits of clean air at no cost or harm to the associate tree species supplying the oxygen.[131] The host and associate relationship is called parasitism if one species benefits while the other suffers. Competition among species or among members of the same species is defined as reciprocal antagonism, such as grasses competing for growth space.[132]
Parasites: A harvestman arachnid is parasitized by mites. This is parasitism because the harvestman is being consumed as its juices are slowly sucked out while the mites gain all the benefits traveling on and feeding off of their host.

Popular ecological study systems for mutualism include, fungus-growing ants employing agricultural symbiosis, bacteria living in the guts of insects and other organisms, the fig wasp and yucca moth pollination complex, lichens with fungi and photosynthetic algae, and corals with photosynthetic algae.[133][134]
Biogeography

The word biogeography is an amalgamation of biology and geography. Biogeography is the comparative study of the geographic distribution of organisms and the corresponding evolution of their traits in space and time.[135] The Journal of Biogeography was established in 1974.[136] Biogeography and ecology share many of their disciplinary roots. For example, the theory of island biogeography, published by the mathematician Robert MacArthur and ecologist Edward O. Wilson in 1967[137] is considered one of the fundamentals of ecological theory.[138]

Biogeography has a long history in the natural sciences where questions arise concerning the spatial distribution of plants and animals. Ecology and evolution provide the explanatory context for biogeographical studies.[135] Biogeographical patterns result from ecological processes that influence range distributions, such as migration and dispersal.[138] and from historical processes that split populations or species into different areas.[139] The biogeographic processes that result in the natural splitting of species explains much of the modern distribution of the Earth's biota. The splitting of lineages in a species is called vicariance biogeography and it is a sub-discipline of biogeography.[139][140][141] There are also practical applications in the field of biogeography concerning ecological systems and processes. For example, the range and distribution of biodiversity and invasive species responding to climate change is a serious concern and active area of research in context of global warming.[41][142]
Molecular ecology

The important relationship between ecology and genetic inheritance predates modern techniques for molecular analysis. Molecular ecological research became more feasible with the development of rapid and accessible genetic technologies, such as the polymerase chain reaction (PCR). The rise of molecular technologies and influx of research questions into this new ecological field resulted in the publication Molecular Ecology in 1992.[145] Molecular ecology uses various analytical techniques to study genes in an evolutionary and ecological context. In 1994, John Avise also played a leading role in this area of science with the publication of his book, Molecular Markers, Natural History and Evolution.[146] Newer technologies opened a wave of genetic analysis into organisms once difficult to study from an ecological or evolutionary standpoint, such as bacteria, fungi and nematodes.

Molecular ecology engendered a new research paradigm to investigate ecological questions considered otherwise intractable. Molecular investigations revealed previously obscured details in the tiny intricacies of nature and improved resolution into probing questions about behavioral and biogeographical ecology. For example, molecular ecology revealed promiscuous sexual behavior and multiple male partners in tree swallows previously thought to be socially monogamous.[147] In a biogeographical context, the marriage between genetics, ecology and evolution resulted in a new sub-discipline called phylogeography.[148]
Relation to the environment

The environment is dynamically interlinked, imposed upon and constrains organisms at any time throughout their life cycle.[149] Like the term ecology, environment has different conceptual meanings and to many these terms also overlap with the concept of nature. Environment "...includes the physical world, the social world of human relations and the built world of human creation."[150]:62 The environment in ecosystems includes both physical parameters and biotic attributes. The physical environment is external to the level of biological organization under investigation, including abiotic factors such as temperature, radiation, light, chemistry, climate and geology. The biotic environment includes genes, cells, organisms, members of the same species (conspecifics) and other species that share a habitat.[151] The laws of thermodynamics applies to ecology by means of its physical state. Armed with an understanding of metabolic and thermodynamic principles a complete accounting of energy and material flow can be traced through an ecosystem.[152]

Environmental and ecological relations are studied through reference to conceptually manageable and isolated parts. Once the effective environmental components are understood they conceptually link back together as a holocoenotic[153] system. In other words, the organism and the environment form a dynamic whole (or umwelt).[154]:252 Change in one ecological or environmental factor can concurrently affect the dynamic state of an entire ecosystem.[155][156]

Ecological studies are necessarily holistic as opposed to reductionistic.[27][157] Holism has three scientific meanings or uses that identify with: 1) the mechanistic complexity of ecosystems, 2) the practical description of patterns in quantitative reductionist terms where correlations may be identified but nothing is understood about the causal relations without reference to the whole system, which leads to 3) a metaphysical hierarchy whereby the causal relations of larger systems are understood without reference to the smaller parts. An example of the metaphysical aspect to holism is the trend of increased exterior thickness in shells of different species. The reason for a thickness increase can be understood through reference to principals of natural selection via predation without any reference to the biomolecular properties of the exterior shells.[158]
Metabolism and the early atmosphere

The Earth formed approximately 4.5 billion years ago[160] and environmental conditions were too extreme for life to form for the first 500 million years. During this early Hadean period, the Earth started to cool, allowing a crust and oceans to form. Environmental conditions were unsuitable for the origins of life for the first billion years after the Earth formed. The Earth's atmosphere transformed from being dominated by hydrogen, to one composed mostly of methane and ammonia. Over the next billion years the metabolic activity of life transformed the atmosphere to higher concentrations of carbon dioxide, nitrogen, and water vapor. These gases changed the way that light from the sun hit the Earth's surface and greenhouse effects trapped heat. There were untapped sources of free energy within the mixture of reducing and oxidizing gasses that set the stage for primitive ecosystems to evolve and, in turn, the atmosphere also evolved.[161]
The leaf is the primary site of photosynthesis in most plants.

Throughout history, the Earth's atmosphere and biogeochemical cycles have been in a dynamic equilibrium with planetary ecosystems. The history is characterized by periods of significant transformation followed by millions of years of stability.[162] The evolution of the earliest organisms, likely anaerobic methanogen microbes, started the process by converting atmospheric hydrogen into methane (4H2 + CO2 → CH4 + 2H2O). Anoxygenic photosynthesis converting hydrogen sulfide into other sulfur compounds or water (2H2S + CO2 → hv → CH2O → H2O → + 2S or 2H2 + CO2 + hv → CH2O + H2O), as occurs in deep sea hydrothermal vents today, reduced hydrogen concentrations and increased atmospheric methane. Early forms of fermentation also increased levels of atmospheric methane. The transition to an oxygen dominant atmosphere (the Great Oxidation) did not begin until approximately 2.4-2.3 billion years ago, but photosynthetic processes started 0.3 to 1 billion years prior.[162][163]
Radiation: heat, temperature and light

The biology of life operates within a certain range of temperatures. Heat is a form of energy that regulates temperature. Heat affects growth rates, activity, behavior and primary production. Temperature is largely dependent on the incidence of solar radiation. The latitudinal and longitudinal spatial variation of temperature greatly affects climates and consequently the distribution of biodiversity and levels of primary production in different ecosystems or biomes across the planet. Heat and temperature relate importantly to metabolic activity. Poikilotherms, for example, have a body temperature that is largely regulated and dependent on the temperature of the external environment. In contrast, homeotherms regulate their internal body temperature by expending metabolic energy.[7][112][152]

There is a relationship between light, primary production, and ecological energy budgets. Sunlight is the primary input of energy into the planet's ecosystems. Light is composed of electromagnetic energy of different wavelengths. Radiant energy from the sun generates heat, provides photons of light measured as active energy in the chemical reactions of life, and also acts as a catalyst for genetic mutation.[7][112][152] Plants, algae, and some bacteria absorb light and assimilate the energy through photosynthesis. Organisms capable of assimilating energy by photosynthesis or through inorganic fixation of H2S are autotrophs. Autotrophs—responsible for primary production—assimilate light energy that becomes metabolically stored as potential energy in the form of biochemical enthalpic bonds.[7][112][152]
Physical environments
Water
The rate of diffusion of carbon dioxide and oxygen is approximately 10,000 times slower in water than it is in air. When soils become flooded, they quickly lose oxygen and transform into a low-concentration (hypoxic -with less than 2 mg O2l−1) environment and eventually become completly (anoxic) environment where anaerobic bacteria thrive among the roots. Water also influences the spectral composition and amount of light as it reflects off the water surface and submerged particles.[164] Aquatic plants exhibit a wide variety of morphological and physiological adaptations that allow them to survive, compete and diversify these environments. For example, the roots and stems develop large air spaces (Aerenchyma) that regulate the efficient transportation gases (for example, CO2 and O2) used in respiration and photosynthesis. In drained soil, microorganisms use oxygen during respiration. In aquatic environments, anaerobic soil microorganisms use nitrate, manganese ions, ferric ions, sulfate, carbon dioxide and some organic compounds. The activity of soil microorganisms and the chemistry of the water reduces the oxidation-reduction potentials of the water. Carbon dioxide, for example, is reduced to methane (CH4) by methanogenic bacteria. Salt water plants (or halophytes) have specialized physiological adaptations, such as the development of special organs for shedding salt and osmo-regulate their internal salt (NaCl) concentrations, to live in estuarine, brackish, or oceanic environments.[164] The physiology of fish is also specially adapted to deal with high levels of salt through osmoregulation. Their gills form electrochemical gradients that mediate salt excresion in saline environments and uptake in fresh water.[165]
Gravity
The shape and energy of the land is affected to a large degree by gravitational forces. On a larger scale, the distribution of gravitational forces on the earth are uneven and influence the shape and movement of tectonic plates as well as having an influence on geomorphic processes such as orogeny and erosion. These forces govern many of the geophysical properties and distributions of ecological biomes across the Earth. On a organism scale, gravitational forces provide directional cues for plant and fungal growth (gravitropism), orientation cues for animal migrations, and influence the biomechanics and size of animals.[7] Ecological traits, such as allocation of biomass in trees during growth are subject to mechanical failure as gravitational forces influence the position and structure of branches and leaves.[166] The cardiovascular systems of all animals are functionally adapted to overcome pressure and gravitational forces that change according to the features of organisms (e.g., height, size, shape), their behavior (e.g., diving, running, flying), and the habitat occupied (e.g., water, hot deserts, cold tundra).[167]
Pressure
Climatic and osmotic pressure places physiological constraints on organisms, such as flight and respiration at high altitudes, or diving to deep ocean depths. These constraints influence vertical limits of ecosystems in the biosphere as organisms are physiologically sensitive and adapted to atmospheric and osmotic water pressure differences.[7] Oxygen levels, for example, decrease with increasing pressure and are a limiting factor for life at higher altitudes.[168] Water transportation through trees is another important ecophysiological parameter where osmotic pressure gradients factor in.[169][170][171] Water pressure in the depths of oceans requires that organisms adapt to these conditions. For example, mammals, such as whales, dolphins and seals are specially adapted to deal with changes in sound due to water pressure differences.[172] Different species of hagfish provide another example of adaptation to deep-sea pressure through specialized protein adaptations.[173]
Wind and turbulence

Turbulent forces in air and water have significant effects on the environment and ecosystem distribution, form and dynamics. On a planetary scale, ecosystems are affected by circulation patterns in the global trade winds. Wind power and the turbulent forces it creates can influence heat, nutrient, and biochemical profiles of ecosystems.[7] For example, wind running over the surface of a lake creates turbulence, mixing the water column and influencing the environmental profile to create thermally layered zones, partially governing how fish, algae, and other parts of the aquatic ecology are structured.[176][177] Wind speed and turbulence also exert influence on rates of evapotranspiration rates and energy budgets in plants and animals.[164][178] Wind speed, temperature and moisture content can vary as winds travel across different landfeatures and elevations. The westerlies, for example, come into contact with the coastal and interior mountains of western North America to produce a rain shadow on the leeward side of the mountain. The air expands and moisture condenses as the winds move up in elevation which can cause precipitation; this is called orographic lift. This environmental process produces spatial divisions in biodiversity, as species adapted to wetter conditions are range-restricted to the coastal mountain valleys and unable to migrate across the xeric ecosystems of the Columbia Basin to intermix with sister lineages that are segregated to the interior mountain systems.[179][180]
Fire

Plants convert carbon dioxide into biomass and emit oxygen into the atmosphere.[181] Approximately 350 million years ago (near the Devonian period) the photosynthetic process brought the concentration of atmospheric oxygen above 17%, which allowed combustion to occur.[182] Fire releases CO2 and converts fuel into ash and tar. Fire is a significant ecological parameter that raises many issues pertaining to its control and suppression in management.[183] While the issue of fire in relation to ecology and plants has been recognized for a long time,[184] Charles Cooper brought attention to the issue of forest fires in relation to the ecology of forest fire suppression and management in the 1960s.[185][186]

Fire creates environmental mosaics and a patchiness to ecosystem age and canopy structure. Native North Americans were among the first to influence fire regimes by controlling their spread near their homes or by lighting fires to stimulate the production of herbaceous foods and basketry materials.[187] The altered state of soil nutrient supply and cleared canopy structure also opens new ecological niches for seedling establishment.[188][189] Most ecosystem are adapted to natural fire cycles. Plants, for example, are equipped with a variety of adaptations to deal with forest fires. Some species (e.g., Pinus halepensis) cannot germinate until after their seeds have lived through a fire. This environmental trigger for seedlings is called serotiny.[190] Some compounds from smoke also promote seed germination.[191] Fire plays a major role in the persistence and resilience of ecosystems.[192]
Biogeochemistry

Ecologists study and measure nutrient budgets to understand how these materials are regulated and flow through the environment.[7][112][152] This research has led to an understanding that there is a global feedback between ecosystems and the physical parameters of this planet including minerals, soil, pH, ions, water and atmospheric gases. There are six major elements, including H (hydrogen), C (carbon), N (nitrogen), O (oxygen), S (sulfur), and P (phosphorus) that form the constitution of all biological macromolecules and feed into the Earth's geochemical processes. From the smallest scale of biology the combined effect of billions upon billions of ecological processes amplify and ultimately regulate the biogeochemical cycles of the Earth. Understanding the relations and cycles mediated between these elements and their ecological pathways has significant bearing toward understanding global biogeochemistry.[193]

The ecology of global carbon budgets gives one example of the linkage between biodiversity and biogeochemistry. For starters, the Earth's oceans are estimated to hold 40,000 gigatonnes (Gt) carbon, vegetation and soil is estimated to hold 2070 Gt carbon, and fossil fuel emissions are estimated to emit an annual flux of 6.3 Gt carbon.[194] At different times in the Earth's history there has been major restructuring in these global carbon budgets that was regulated to a large extent by the ecology of the land. For example, through the early-mid Eocene volcanic outgassing, the oxidation of methane stored in wetlands, and seafloor gases increased atmospheric CO2 concentrations to levels as high as 3500 ppm.[195] In the Oligocene, from 25 to 32 million years ago, there was another significant restructuring in the global carbon cycle as grasses evolved a special type of C4 photosynthesis and expanded their ranges. This new photosynthetic pathway evolved in response to the drop in atmospheric CO2 concentrations below 550 ppm.[196] Ecosystem functions such as these feed back significantly into global atmospheric models for carbon cycling. Loss in the abundance and distribution of biodiversity causes global carbon cycle feedbacks that are expected to increase rates of global warming in the next century.[197] The effect of global warming melting large sections of permafrost creates a new mosaic of flooded areas where decomposition results in the emission of methane (CH4). Hence, there is a relationship between global warming, decomposition and respiration in soils and wetlands producing significant climate feedbacks and altered global biogeochemical cycles.[198][199] There is concern over increases in atmospheric methane in the context of the global carbon cycle, because methane is also a greenhouse gas that is 23 times more effective at absorbing long-wave radiation than CO2 on a 100 year time scale.[200]
Human ecology
Ecosystem services

The ecosystems of planet Earth are coupled to human environments. Ecosystems regulate the global geophysical cycles of energy, climate, soil nutrients, and water that in turn support and grow natural capital (including the environmental, physiological, cognitive, cultural, and spiritual dimensions of life). Ultimately, every manufactured product in human environments comes from natural systems.[223] Ecosystems are considered common-pool resources because ecosystems do not exclude beneficiaries and they can be depleted or degraded.[228] For example, green space within communities provides sustainable health services that reduces mortality and regulates the spread of vector borne disease.[229] Research shows that people who are more engaged with regular access to natural areas have lower rates of diabetes, heart disease and psychological disorders.[230] These ecological health services are regularly depleted through urban development projects that do not factor in the common-pool value of ecosystems.[231][232]

The ecological commons delivers a diverse supply of community services that sustains the well-being of human society.[233][234] The Millennium Ecosystem Assessment, an international UN initiative involving more than 1,360 experts worldwide, identifies four main ecosystem service types having 30 sub-categories stemming from natural capital. The ecological commons includes provisioning (e.g., food, raw materials, medicine, water supplies), regulating (e.g., climate, water, soil retention, flood retention), cultural (e.g., science and education, artistic, spiritual), and supporting (e.g., soil formation, nutrient cycling, water cycling) services.[10]
Sixth mass extinction

Global assessments of biodiversity indicate that the current epoch, the Holocene (or Anthropocene)[236] is a sixth mass extinction.[237] Species loss is accelerating at 100–1000 times faster than average background rates in the fossil record.[238][239] The field of conservation biology involves ecologists that are researching, confronting, and searching for solutions to sustain the planet's ecosystems for future generations.[240]

"Human activities are associated directly or indirectly with nearly every aspect of the current extinction spasm."[238]:11472

Nature is a resilient system. Ecosystems regenerate, withstand, and are forever adapting to fluctuating environments. Ecological resilience is an important conceptual framework in conservation management and it is defined as the preservation of biological relations in ecosystems that persevere and regenerate in response to disturbance over time. Disturbances, such as fire, are both cause and product of natural fluctuations in death rates, species assemblages, and biomass densities within an ecological community. These disturbances create places of renewal where new directions emerge out of the patchwork of natural experimentation and opportunity.[192][241] [242] However, persistent, systematic, large and nonrandom disturbance caused by the niche constructing behavior of human beings, habitat conversion and land development, has pushed many of the Earth's ecosystems to the extent of their resilient thresholds. Three planetary thresholds have already been crossed, including 1) biodiversity loss, 2) climate change, and 3) nitrogen cycles. These biophysical systems are ecologically interrelated and naturally resilient, but human civilization has transitioned the planet to the Anthropocene epoch, where the threshold for planetary scale resilience has been crossed and the ecological state of the Earth is deteriorating rapidly to the detriment of humanity.[243] The world's fisheries and oceans, for example, are facing dire challenges as the threat of global collapse appears imminent, with serious ramifications for the well-being of humanity.[244] The ecology of the planet is further threatened by global warming, but investments in nature conservation can provide a regulatory feedback to store and regulate carbon and other greenhouse gases.[245][246]
Ecological footprint
In 1992, William Rees developed the ecological footprint concept. The ecological footprint and its close analog the water footprint has become a popular way of accounting for the level of impact that human society is imparting on the Earth's ecosystems.[247][248] All indications are that the human enterprise is unsustainable as the footprint of society is placing too much stress on the ecology of the planet.[249] The WWF 2008 living planet report and other researchers report that human civilization has exceeded the bio-regenerative capacity of the planet.[249][250] This means that the footprint of human consumption is extracting more natural resources than can be replenished by ecosystems around the world.
Ecological economics
Ecological economics is an economic science that extends its methods of valuation onto nature in an effort to address the inequity between market growth and biodiversity loss.[11] Natural capital is the stock of materials or information stored in biodiversity that generates services that can enhance the welfare of communities.[251] Population losses are the more sensitive indicator of natural capital than are species extinction in the accounting of ecosystem services. The prospect for recovery in the economic crisis of nature is grim. Populations, such as local ponds and patches of forest are being cleared away and lost at rates that exceed species extinctions.[42] The mainstream growth-based economic system adopted by governments worldwide does not include a price or markets for natural capital. This type of economic system places further ecological debt onto future generations.[252][253]

Human societies are increasingly being placed under stress as the ecological commons is diminished through an accounting system that has incorrectly assumed "... that nature is a fixed, indestructible capital asset."[254]:44 The current wave of threats, including massive extinction rates and concurrent loss of natural capital to the detriment of human society, is happening rapidly. This is called a biodiversity crisis, because 50% of the worlds species are predicted to go extinct within the next 50 years.[255][256] Conventional monetary analyses are unable to detect or deal with these sorts of ecological problems.[257] Multiple global ecological economic initiatives are being promoted to solve this problem. For example, governments of the G8 met in 2007 and set forth The Economics of Ecosystems and Biodiversity (TEEB) initiative:

In a global study we will initiate the process of analyzing the global economic benefit of biological diversity, the costs of the loss of biodiversity and the failure to take protective measures versus the costs of effective conservation.[258]
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