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Friday, October 16, 2026

Evolutionary medicine

From Wikipedia, the free encyclopedia
The bacterium Mycobacterium tuberculosis can evolve to subvert the protection offered by immune defenses

Evolutionary medicine or Darwinian medicine is the application of modern evolutionary theory to understanding health and disease. Modern biomedical research and practice have focused on the molecular and physiological mechanisms underlying health and disease, while evolutionary medicine focuses on the question of why evolution has shaped these mechanisms in ways that may leave us susceptible to disease. The evolutionary approach has driven important advances in the understanding of cancer, autoimmune disease, and anatomy. Medical schools have been slower to integrate evolutionary approaches because of limitations on what can be added to existing medical curricula. The International Society for Evolution, Medicine and Public Health coordinates efforts to develop the field. It owns the Oxford University Press journal Evolution, Medicine and Public Health and The Evolution and Medicine Review.

Core principles

Utilizing the Delphi method, 56 experts from a variety of disciplines, including anthropology, medicine, nursing, and biology agreed upon 14 core principles intrinsic to the education and practice of evolutionary medicine. These 14 principles can be further grouped into five general categories: question framing, evolution I and II (with II involving a higher level of complexity), evolutionary trade-offs, reasons for vulnerability, and culture. Additional information regarding these principles may be found in the table below.

Core Principles of Evolutionary Medicine
Topic Core Principle
Types of explanation (question framing) Both proximate (mechanistic) and ultimate (evolutionary) explanations are needed to provide a full biological understanding of traits, including those that increase vulnerability to disease.
Evolutionary processes (evolution I) All evolutionary processes, including natural selection, genetic drift, mutation, migration and non-random mating, are important for understanding traits and disease.
Reproductive success (evolution I) Natural selection maximizes reproductive success, sometimes at the expense of health and longevity.
Sexual selection (evolution I) Sexual selection shapes traits that result in different health risks between sexes.
Constraints (evolution I) Several constraints inhibit the capacity of natural selection to shape traits that are hypothetically optimal for health.
Trade-offs (evolutionary trade-offs) Evolutionary changes in one trait that improve fitness can be linked to changes in other traits that decrease fitness.
Life History Theory (evolutionary trade-offs) Life history traits, such as age at first reproduction, reproductive lifespan and rate of senescence, are shaped by evolution, and have implications for health and disease.
Levels of selection (evolution II) Vulnerabilities to disease can result when selection has opposing effects at different levels (e.g. genetic elements, cells, organisms, kin and other levels).
Phylogeny (evolution II) Tracing phylogenetic relationships for species, populations, traits or pathogens can provide insights into health and disease.
Coevolution (evolution II) Coevolution among species can influence health and disease (e.g. evolutionary arms races and mutualistic relationships such as those seen in the microbiome).
Plasticity (evolution II) Environmental factors can shift developmental trajectories in ways that influence health and the plasticity of these trajectories can be the product of evolved adaptive mechanisms.
Defenses (reasons for vulnerability) Many signs and symptoms of disease (e.g. fever) are useful defenses, which can be pathological if dysregulated.
Mismatch (reasons for vulnerability) Disease risks can be altered for organisms living in environments that differ from those in which their ancestors evolved.
Cultural practices (culture) Cultural practices can influence the evolution of humans and other species (including pathogens), in ways that can affect health and disease (e.g. anti-biotic use, birth practices, diet, etc.).

Human adaptations

Adaptation works within constraints, makes compromises and trade-offs, and occurs in the context of different forms of competition.

Constraints

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

  • DNA cannot be totally prevented from undergoing somatic replication corruption; this has meant that cancer, which is caused by somatic mutations, has not (so far) been eliminated by natural selection.
  • Humans cannot biosynthesize vitamin C, and so risk scurvy, vitamin C deficiency disease, if dietary intake of the vitamin is insufficient.
  • Retinal neurons and their axon output have evolved to be inside the layer of retinal pigment cells. This creates a constraint on the evolution of the visual system such that the optic nerve is forced to exit the retina through a point called the optic disc. This, in turn, creates a blind spot. More importantly, it makes vision vulnerable to increased pressure within the eye (glaucoma) since this cups and damages the optic nerve at this point, resulting in impaired vision.

Other constraints occur as the byproduct of adaptive innovations.

Trade-offs and conflicts

One constraint upon selection is that different adaptations can conflict, which requires a compromise between them to ensure an optimal cost-benefit tradeoff.

Competition effects

Different forms of competition exist and these can shape the processes of genetic change.

Lifestyle

Humans evolved to live as simple hunter-gatherers in small tribal bands, while contemporary humans have a more complex life. This change may make present-day humans susceptible to lifestyle diseases.

Diet

In contrast to the diet of early hunter-gatherers, the modern Western diet often contains high quantities of fat, salt, and simple carbohydrates, such as refined sugars and flours.

Among different countries, the incidence of colon cancer varies widely, and the extent of exposure to a Western pattern diet may be a factor in cancer incidence.

Life expectancy

Examples of aging-associated diseases are atherosclerosis and cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension and Alzheimer's disease. The incidence of all of these diseases increases rapidly with aging (increases exponentially with age, in the case of cancer).

Age-Specific SEER Incidence Rates, 2003-2007

Of the roughly 150,000 people who die each day across the globe, about two thirds—100,000 per day—die of age-related causes. In industrialized nations, the proportion is much higher, reaching 90%.

Exercise

Many contemporary humans engage in little physical exercise compared to the physically active lifestyles of ancestral hunter-gatherers. Prolonged periods of inactivity may have only occurred in early humans following illness or injury, so a modern sedentary lifestyle may continuously cue the body to trigger life preserving metabolic and stress-related responses such as inflammation, and some theorize that this causes chronic diseases.

Cleanliness

Contemporary humans in developed countries are mostly free of parasites, particularly intestinal ones. This is largely due to frequent washing of clothing and the body, and improved sanitation. Although such hygiene can be very important when it comes to maintaining good health, it can be problematic for the proper development of the immune system. The hygiene hypothesis is that humans evolved to be dependent on certain microorganisms that help establish the immune system, and modern hygiene practices can prevent necessary exposure to these microorganisms. "Microorganisms and macroorganisms such as helminths from mud, animals, and feces play a critical role in driving immunoregulation" (Rook, 2012). Essential microorganisms play a crucial role in building and training immune functions that fight off and repel some diseases, and protect against excessive inflammation, which has been implicated in several diseases. For instance, recent studies have found evidence supporting inflammation as a contributing factor in Alzheimer's Disease.

Specific explanations

This is a partial list: all links here go to a section describing or debating its evolutionary origin.

Other

Evolutionary psychology

As noted in the table below, adaptationist hypotheses regarding the etiology of psychological disorders are often based on analogies with evolutionary perspectives on medicine and physiological dysfunctions (see in particular, Randy Nesse and George C. Williams' book Why We Get Sick). Evolutionary psychiatrists and psychologists suggest that some mental disorders likely have multiple causes.

Possible Causes of Psychological 'Abnormalities' from an Adaptationist Perspective

Summary based on information in Buss (2011), Gaulin & McBurney (2004), Workman & Reader (2004)

Possible cause Physiological DysfunctionPsychological Dysfunction
Functioning adaptation
(adaptive defense)		Fever / Vomiting
(functional responses to infection or ingestion of toxins)		Mild depression or anxiety
(functional responses to mild loss or stress)
By-product of an adaptation(s)Intestinal gas
(byproduct of digestion of fiber)		Sexual fetishes (?)
(possible byproduct of normal sexual arousal adaptations that have 'imprinted' on unusual objects or situations)
Adaptations with multiple effectsGene for malaria resistance, in homozygous form, causes sickle cell anemiaAdaptation(s) for high levels of creativity may also predispose schizophrenia or bi-polar disorder
(adaptations with both positive and negative effects, perhaps dependent on alternate developmental trajectories)
Malfunctioning adaptationAllergies
(over-reactive immunological responses)		Autism
(possible malfunctioning of theory of mind module)
Frequency-dependent morphsThe two sexes / Different blood and immune system typesPersonality traits and personality disorders
(may represent alternative behavioral strategies dependent on the frequency of the strategy in the population)
Mismatch between ancestral & current environmentsModern diet-related Type 2 DiabetesMore frequent modern interaction with strangers (compared to family and close friends) may predispose greater incidence of depression & anxiety
Tails of normal (bell shaped) curveVery short or tall heightTails of the distribution of personality traits (e.g., extremely introverted or extroverted)

See several topic areas, and the associated references, below.

History

Charles Darwin

Charles Darwin did not discuss the implications of his work for medicine, though biologists quickly appreciated the germ theory of disease and its implications for understanding the evolution of pathogens, as well as an organism's need to defend against them.

Medicine, in turn, ignored evolution, and instead focused (as done in the hard sciences) upon proximate mechanical causes.

medicine has modelled itself after a mechanical physics, deriving from Galileo, Newton, and Descartes.... As a result of assuming this model, medicine is mechanistic, materialistic, reductionistic, linear-causal, and deterministic (capable of precise predictions) in its concepts. It seeks explanations for diseases, or their symptoms, signs, and cause in single, materialistic— i.e., anatomical or structural (e.g., in genes and their products)— changes within the body, wrought directly (linearly), for example, by infectious, toxic, or traumatic agents.

George C. Williams was the first to apply evolutionary theory to health in the context of senescence. Also in the 1950s, John Bowlby approached the problem of disturbed child development from an evolutionary perspective upon attachment.

An important theoretical development was Nikolaas Tinbergen's distinction made originally in ethology between evolutionary and proximate mechanisms.

Randolph M. Nesse summarizes its relevance to medicine:

all biological traits need two kinds of explanation, both proximate and evolutionary. The proximate explanation for a disease describes what is wrong in the bodily mechanism of individuals affected by it. An evolutionary explanation is completely different. Instead of explaining why people are different, it explains why we are all the same in ways that leave us vulnerable to disease. Why do we all have wisdom teeth, an appendix, and cells that can divide out of control?

The paper of Paul Ewald in 1980, "Evolutionary Biology and the Treatment of Signs and Symptoms of Infectious Disease", and that of Williams and Nesse in 1991, "The Dawn of Darwinian Medicine" were key developments. The latter paper "draw a favorable reception", and led to a book, Why We Get Sick (published as Evolution and healing in the UK). In 2008, an online journal started: Evolution and Medicine Review.

In 2000, Paul Sherman hypothesised that morning sickness could be an adaptation that protects the developing fetus from foodborne illnesses, some of which can cause miscarriage or birth defects, such as listeriosis and toxoplasmosis.

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Evolvability

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Evolvability
Visualization of two dimensions of a NK fitness landscape. The X and Y axes represent a combination of bits that encode the genotype. The height of the peaks represents the fitness, or reproductive success, or organisms with that particular genotype. The paths drawn on the landscape represent different paths that a population could follow while evolving on this fitness landscape.

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

In order for a biological organism to evolve by natural selection, there must be a certain minimum probability that new, heritable variants are beneficial. Random mutations, unless they occur in DNA sequences with no function, are expected to be mostly detrimental. Beneficial mutations are always rare, but if they are too rare, then adaptation cannot occur. Early failed efforts to evolve computer programs by random mutation and selection showed that evolvability is not a given, but depends on the representation of the program as a data structure, because this determines how changes in the program map to changes in its behavior. Analogously, the evolvability of organisms depends on their genotype–phenotype map. This means that genomes are structured in ways that make beneficial changes more likely. This has been taken as evidence that evolution has created fitter populations of organisms that are better able to evolve.

Alternative definitions

Andreas Wagner describes two definitions of evolvability. According to the first definition, a biological system is evolvable:

  • if its properties show heritable genetic variation, and
  • if natural selection can thus change these properties.

According to the second definition, a biological system is evolvable:

  • if it can acquire novel functions through genetic change, functions that help the organism survive and reproduce.

For example, consider an enzyme with multiple alleles in the population. Each allele catalyzes the same reaction, but with a different level of activity. However, even after millions of years of evolution, exploring many sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a different reaction. Thus, although the enzyme's activity is evolvable in the first sense, that does not mean that the enzyme's function is evolvable in the second sense. However, every system evolvable in the second sense must also be evolvable in the first.

Massimo Pigliucci recognizes three classes of definition, depending on timescale. The first corresponds to Wagner's first, and represents the very short timescales that are described by quantitative genetics. He divides Wagner's second definition into two categories, one representing the intermediate timescales that can be studied using population genetics, and one representing exceedingly rare long-term innovations of form.

Pigliucci's second definition of evolvability includes Altenberg's quantitative concept of evolvability, being not a single number, but the entire upper tail of the fitness distribution of the offspring produced by the population. This quantity was considered a "local" property of the instantaneous state of a population, and its integration over the population's evolutionary trajectory, and over many possible populations, would be necessary to give a more global measure of evolvability.

Generating more variation

More heritable phenotypic variation means more evolvability. While mutation is the ultimate source of heritable variation, its permutations and combinations also make a big difference. Sexual reproduction generates more variation (and thereby evolvability) relative to asexual reproduction (see evolution of sexual reproduction). Evolvability is further increased by generating more variation when an organism is stressed, and thus likely to be less well adapted, but less variation when an organism is doing well. The amount of variation generated can be adjusted in many different ways, for example via the mutation rate, via the probability of sexual vs. asexual reproduction, via the probability of outcrossing vs. inbreeding, via dispersal, and via access to previously cryptic variants through the switching of an evolutionary capacitor. A large population size increases the influx of novel mutations in each generation.

Robustness and evolvability

The relationship between robustness and evolvability depends on whether recombination can be ignored. Recombination can generally be ignored in asexual populations and for traits affected by single genes.

Without recombination

Robustness in the face of mutation does not increase evolvability in the first sense. In organisms with a high level of robustness, mutations have smaller phenotypic effects than in organisms with a low level of robustness. Thus, robustness reduces the amount of heritable genetic variation on which selection can act. However, robustness may allow exploration of large regions of genotype space, increasing evolvability according to the second sense. Even without genetic diversity, some genotypes have higher evolvability than others, and selection for robustness can increase the "neighborhood richness" of phenotypes that can be accessed from the same starting genotype by mutation. For example, one reason many proteins are less robust to mutation is that they have marginal thermodynamic stability, and most mutations reduce this stability further. Proteins that are more thermostable can tolerate a wider range of mutations and are more evolvable. For polygenic traits, neighborhood richness contributes more to evolvability than does genetic diversity or "spread" across genotype space.

With recombination

Temporary robustness, or canalisation, may lead to the accumulation of significant quantities of cryptic genetic variation. In a new environment or genetic background, this variation may be revealed and sometimes be adaptive.

Factors affecting evolvability via robustness

Different genetic codes have the potential to change robustness and evolvability by changing the effect of single-base mutational changes.

Exploration ahead of time

When mutational robustness exists, many mutants will persist in a cryptic state. Mutations tend to fall into two categories, having either a very bad effect or very little effect: few mutations fall somewhere in between. Sometimes, these mutations will not be completely invisible, but still have rare effects, with very low penetrance. When this happens, natural selection weeds out the very bad mutations, while leaving the others relatively unaffected. While evolution has no "foresight" to know which environment will be encountered in the future, some mutations cause major disruption to a basic biological process, and will never be adaptive in any environment. Screening these out in advance leads to preadapted stocks of cryptic genetic variation.

Another way that phenotypes can be explored, prior to strong genetic commitment, is through learning. An organism that learns gets to "sample" several different phenotypes during its early development, and later sticks to whatever worked best. Later in evolution, the optimal phenotype can be genetically assimilated so it becomes the default behavior rather than a rare behavior. This is known as the Baldwin effect, and it can increase evolvability.

Learning biases phenotypes in a beneficial direction. But an exploratory flattening of the fitness landscape can also increase evolvability even when it has no direction, for example when the flattening is a result of random errors in molecular and/or developmental processes. This increase in evolvability can happen when evolution is faced with crossing a "valley" in an adaptive landscape. This means that two mutations exist that are deleterious by themselves, but beneficial in combination. These combinations can evolve more easily when the landscape is first flattened, and the discovered phenotype is then fixed by genetic assimilation.

Exploration ahead of time

When mutational robustness exists, many mutants will persist in a cryptic state. Mutations tend to fall into two categories, having either a very bad effect or very little effect: few mutations fall somewhere in between. Sometimes, these mutations will not be completely invisible, but still have rare effects, with very low penetrance. When this happens, natural selection weeds out the very bad mutations, while leaving the others relatively unaffected. While evolution has no "foresight" to know which environment will be encountered in the future, some mutations cause major disruption to a basic biological process, and will never be adaptive in any environment. Screening these out in advance leads to preadapted stocks of cryptic genetic variation.

Another way that phenotypes can be explored, prior to strong genetic commitment, is through learning. An organism that learns gets to "sample" several different phenotypes during its early development, and later sticks to whatever worked best. Later in evolution, the optimal phenotype can be genetically assimilated so it becomes the default behavior rather than a rare behavior. This is known as the Baldwin effect, and it can increase evolvability.

Learning biases phenotypes in a beneficial direction. But an exploratory flattening of the fitness landscape can also increase evolvability even when it has no direction, for example when the flattening is a result of random errors in molecular and/or developmental processes. This increase in evolvability can happen when evolution is faced with crossing a "valley" in an adaptive landscape. This means that two mutations exist that are deleterious by themselves, but beneficial in combination. These combinations can evolve more easily when the landscape is first flattened, and the discovered phenotype is then fixed by genetic assimilation.

Modularity

If every mutation affected every trait, then a mutation that was an improvement for one trait would be a disadvantage for other traits. This means that almost no mutations would be beneficial overall. But if pleiotropy is restricted to within functional modules, then mutations affect only one trait at a time, and adaptation is much less constrained. In a modular gene network, for example, a gene that induces a limited set of other genes that control a specific trait under selection may evolve more readily than one that also induces other gene pathways controlling traits not under selection. Individual genes also exhibit modularity. A mutation in one cis-regulatory element of a gene's promoter region may allow the expression of the gene to be altered only in specific tissues, developmental stages, or environmental conditions rather than changing gene activity in the entire organism simultaneously.

Evolution of evolvability

While variation yielding high evolvability could be useful in the long term, in the short term most of that variation is likely to be a disadvantage. For example, naively it would seem that increasing the mutation rate via a mutator allele would increase evolvability. But as an extreme example, if the mutation rate is too high then all individuals will be dead or at least carry a heavy mutation load. Short-term selection for low variation most of the time is likely to be more powerful than long-term selection for evolvability, making it difficult for natural selection to cause the evolution of evolvability. Other forces of selection also affect the generation of variation; for example, mutation and recombination may in part be byproducts of mechanisms to cope with DNA damage.

When recombination is low, mutator alleles may still sometimes hitchhike on the success of adaptive mutations that they cause. In this case, selection can take place at the level of the lineage. This may explain why mutators are often seen during experimental evolution of microbes. Mutator alleles can also evolve more easily when they only increase mutation rates in nearby DNA sequences, not across the whole genome: this is known as a contingency locus.

The evolution of evolvability is less controversial if it occurs via the evolution of sexual reproduction, or via the tendency of variation-generating mechanisms to become more active when an organism is stressed. The yeast prion [PSI+] may also be an example of the evolution of evolvability through evolutionary capacitance. An evolutionary capacitor is a switch that turns genetic variation on and off. This is very much like bet-hedging the risk that a future environment will be similar or different. Theoretical models also predict the evolution of evolvability via modularity. When the costs of evolvability are sufficiently short-lived, more evolvable lineages may be the most successful in the long-term. However, the hypothesis that evolvability is an adaptation is often rejected in favor of alternative hypotheses, e.g. minimization of costs.

Applications

The study of evolvability has practical applications. For protein engineering, high evolvability is desirable, while high evolvability in pathogens and agricultural pests is harmful to human interests. Protein evolvability is defined as the ability of the protein to acquire sequence diversity and conformational flexibility which can enable it to evolve toward a new function.

In protein engineering, both rational design and directed evolution approaches aim to create changes rapidly through mutations with large effects. Such mutations, however, commonly destroy enzyme function or at least reduce tolerance to further mutations. Identifying evolvable proteins and manipulating their evolvability is becoming increasingly necessary in order to achieve ever larger functional modification of enzymes. Proteins are also often studied as part of the basic science of evolvability, because the biophysical properties and chemical functions can be easily changed by a few mutations. More evolvable proteins can tolerate a broader range of amino acid changes and allow them to evolve toward new functions. The study of evolvability has fundamental importance for understanding very long term evolution of protein superfamilies.

Many human pathogens are capable of evolution. Viruses, bacteria, fungi and cancers evolve to be resistant to host immune defences, as well as pharmaceutical drugs. These same problems occur in agriculture with pesticide and herbicide resistance. It is possible that we are facing the end of the effective life of most of available antibiotics. Predicting the evolution and evolvability of our pathogens, and devising strategies to slow or circumvent the development of resistance, demands deeper knowledge of the complex forces driving evolution at the molecular level.

A better understanding of evolvability is proposed to be part of an Extended Evolutionary Synthesis.

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Adaptation

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Adaptation

In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process of natural selection that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the population during that process. Thirdly, it is a phenotypic trait or adaptive trait, with a functional role in each individual organism, that is maintained and has evolved through natural selection.

Historically, adaptation has been described from the time of the ancient Greek philosophers such as Empedocles and Aristotle. In 18th and 19th-century natural theology, adaptation was taken as evidence for the existence of a deity. Charles Darwin and Alfred Russel Wallace proposed instead that it was explained by natural selection.

Adaptation is related to biological fitness, which governs the rate of evolution as measured by changes in allele frequencies. Often, two or more species co-adapt and co-evolve as they develop adaptations that interlock with those of the other species, such as with flowering plants and pollinating insects. In mimicry, species evolve to resemble other species; in mimicry this is a mutually beneficial co-evolution as each of a group of strongly defended species (such as wasps able to sting) come to advertise their defences in the same way. Features evolved for one purpose may be co-opted for a different one, as when the insulating feathers of dinosaurs were co-opted for bird flight.

Adaptation is a major topic in the philosophy of biology, as it concerns function and purpose (teleology). Some biologists try to avoid terms which imply purpose in adaptation, not least because they suggest a deity's intentions, but others note that adaptation is necessarily purposeful.

History

Adaptation is an observable fact of life accepted by philosophers and natural historians from ancient times, independently of their views on evolution, but their explanations differed. Empedocles did not believe that adaptation required a final cause (a purpose), but thought that it "came about naturally, since such things survived." Aristotle did believe in final causes, but assumed that species were fixed.

The second of Jean-Baptiste Lamarck's two factors (the first being a complexifying force) was an adaptive force that causes animals with a given body plan to adapt to circumstances by inheritance of acquired characteristics, creating a diversity of species and genera.

In natural theology, adaptation was interpreted as the work of a deity and as evidence for the existence of God. William Paley believed that organisms were perfectly adapted to the lives they led, an argument that shadowed Gottfried Wilhelm Leibniz, who had argued that God had brought about "the best of all possible worlds." Voltaire's satire Dr. Pangloss is a parody of this optimistic idea, and David Hume also argued against design. Charles Darwin broke with the tradition by emphasising the flaws and limitations which occurred in the animal and plant worlds.

Jean-Baptiste Lamarck proposed a tendency for organisms to become more complex, moving up a ladder of progress, plus "the influence of circumstances", usually expressed as use and disuse. This second, subsidiary element of his theory is what is now called Lamarckism, a proto-evolutionary hypothesis of the inheritance of acquired characteristics, intended to explain adaptations by natural means.

Other natural historians, such as Buffon, accepted adaptation, and some also accepted evolution, without voicing their opinions as to the mechanism. This illustrates the real merit of Darwin and Alfred Russel Wallace, and secondary figures such as Henry Walter Bates, for putting forward a mechanism whose significance had only been glimpsed previously. A century later, experimental field studies and breeding experiments by people such as E. B. Ford and Theodosius Dobzhansky produced evidence that natural selection was not only the 'engine' behind adaptation, but was a much stronger force than had previously been thought.

General principles

The significance of an adaptation can only be understood in relation to the total biology of the species.

What adaptation is

Adaptation is primarily a process rather than a physical form or part of a body. An internal parasite (such as a liver fluke) can illustrate the distinction: such a parasite may have a very simple bodily structure, but nevertheless the organism is highly adapted to its specific environment. From this we see that adaptation is not just a matter of visible traits: in such parasites critical adaptations take place in the life cycle, which is often quite complex. However, as a practical term, "adaptation" often refers to a product: those features of a species which result from the process. Many aspects of an animal or plant can be correctly called adaptations, though there are always some features whose function remains in doubt. By using the term adaptation for the evolutionary process, and adaptive trait for the bodily part or function (the product), one may distinguish the two different senses of the word.

Adaptation is one of the two main processes that explain the observed diversity of species, such as the different species of Darwin's finches. The other process is speciation, in which new species arise, typically through reproductive isolation. An example widely used today to study the interplay of adaptation and speciation is the evolution of cichlid fish in African lakes, where the question of reproductive isolation is complex.

Adaptation is not always a simple matter where the ideal phenotype evolves for a given environment. An organism must be viable at all stages of its development and at all stages of its evolution. This places constraints on the evolution of development, behaviour, and structure of organisms. The main constraint, over which there has been much debate, is the requirement that each genetic and phenotypic change during evolution should be relatively small, because developmental systems are so complex and interlinked. However, it is not clear what "relatively small" should mean, for example polyploidy in plants is a reasonably common large genetic change. The origin of eukaryotic endosymbiosis is a more dramatic example.

All adaptations help organisms survive in their ecological niches. The adaptive traits may be structural, behavioural or physiological. Structural adaptations are physical features of an organism, such as shape, body covering, armament, and internal organization. Behavioural adaptations are inherited systems of behaviour, whether inherited in detail as instincts, or as a neuropsychological capacity for learning. Examples include searching for food, mating, and vocalizations. Physiological adaptations permit the organism to perform special functions such as making venom, secreting slime, and phototropism, but also involve more general functions such as growth and development, temperature regulation, ionic balance and other aspects of homeostasis. Adaptation affects all aspects of the life of an organism.

The following definitions are given by the evolutionary biologist Theodosius Dobzhansky:

1. Adaptation is the evolutionary process whereby populations of organisms become better able to live in a habitat or habitats.
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.
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.

What adaptation is not

The common kestrel has adapted successfully to urban areas

Adaptation differs from flexibility, acclimatization, and learning, all of which are changes during life which are not inherited. Flexibility deals with the relative capacity of an organism to maintain itself in different habitats: its degree of specialization. Acclimatization describes automatic physiological adjustments during life; learning means alteration in behavioural performance during life.

Flexibility stems from phenotypic plasticity, the ability of an organism with a given genotype (genetic type) to change its phenotype (observable characteristics) in response to changes in its habitat, or to move to a different habitat. The degree of flexibility is inherited, and varies between individuals. A highly specialized animal or plant lives only in a well-defined habitat, eats a specific type of food, and cannot survive if its needs are not met. Many herbivores are like this; extreme examples are koalas which depend on Eucalyptus, and giant pandas which require bamboo. A generalist, on the other hand, eats a range of food, and can survive in many different conditions. Examples are humans, rats, crabs and many carnivores. The tendency to behave in a specialized or exploratory manner is inherited—it is an adaptation. Rather different is developmental flexibility: "An animal or plant is developmentally flexible if when it is raised in or transferred to new conditions, it changes in structure so that it is better fitted to survive in the new environment," writes the evolutionary biologist John Maynard Smith.

If humans move to a higher altitude, respiration and physical exertion become a problem, but after spending time in high altitude conditions they acclimatize to the reduced partial pressure of oxygen, such as by producing more red blood cells. The ability to acclimatize is an adaptation, but the acclimatization itself is not. The reproductive rate declines, but deaths from some tropical diseases also go down. Over a longer period of time, some people are better able to reproduce at high altitudes than others. They contribute more heavily to later generations, and gradually by natural selection the whole population becomes adapted to the new conditions. This has demonstrably occurred, as the observed performance of long-term communities at higher altitude is significantly better than the performance of new arrivals, even when the new arrivals have had time to acclimatize.

Adaptedness and fitness

There is a relationship between adaptedness and the concept of fitness used in population genetics. Differences in fitness between genotypes predict the rate of evolution by natural selection. Natural selection changes the relative frequencies of alternative phenotypes, insofar as they are heritable. However, a phenotype with high adaptedness may not have high fitness. Dobzhansky mentioned the example of the Californian redwood, which is highly adapted, but a relict species in danger of extinction. Elliott Sober commented that adaptation was a retrospective concept since it implied something about the history of a trait, whereas fitness predicts a trait's future.

1. Relative fitness. The average contribution to the next generation by a genotype or a class of genotypes, relative to the contributions of other genotypes in the population. This is also known as Darwinian fitness, selection coefficient, and other terms.
2. Absolute fitness. The absolute contribution to the next generation by a genotype or a class of genotypes. Also known as the Malthusian parameter when applied to the population as a whole.
3. Adaptedness. The extent to which a phenotype fits its local ecological niche. Researchers can sometimes test this through a reciprocal transplant.
In this sketch of a fitness landscape, a population can evolve by following the arrows to the adaptive peak at point B, and the points A and C are local optima where a population could become trapped.

Sewall Wright proposed that populations occupy adaptive peaks on a fitness landscape. To evolve to another, higher peak, a population would first have to pass through a valley of maladaptive intermediate stages, and might be "trapped" on a peak that is not optimally adapted.

Types

Adaptation is the heart and soul of evolution.

— Niles Eldredge, Reinventing Darwin: The Great Debate at the High Table of Evolutionary Theory

Changes in habitat

Before Darwin, adaptation was seen as a fixed relationship between an organism and its habitat. It was not appreciated that as the climate changed, so did the habitat; and as the habitat changed, so did the biota. Also, habitats are subject to changes in their biota: for example, invasions of species from other areas. The relative numbers of species in a given habitat are always changing. Change is the rule, though much depends on the speed and degree of the change. When the habitat changes, three main things may happen to a resident population: habitat tracking, genetic change or extinction. In fact, all three things may occur in sequence. Of these three effects only genetic change brings about adaptation. When a habitat changes, the resident population typically moves to more suitable places; this is the typical response of flying insects or oceanic organisms, which have wide (though not unlimited) opportunity for movement. This common response is called habitat tracking. It is one explanation put forward for the periods of apparent stasis in the fossil record (the punctuated equilibrium theory).

Genetic change

Without mutation, the ultimate source of all genetic variation, there would be no genetic changes and no subsequent adaptation through evolution by natural selection. Genetic change occurs in a population when mutation increases or decreases in its initial frequency followed by random genetic drift, migration, recombination or natural selection act on this genetic variation. One example is that the first pathways of enzyme-based metabolism at the very origin of life on Earth may have been co-opted components of the already-existing purine nucleotide metabolism, a metabolic pathway that evolved in an ancient RNA world. The co-option requires new mutations and through natural selection, the population then adapts genetically to its present circumstances. Genetic changes may result in entirely new or gradual change to visible structures, or they may adjust physiological activity in a way that suits the habitat. The varying shapes of the beaks of Darwin's finches, for example, are driven by adaptive mutations in the ALX1 gene. The coat color of different wild mouse species matches their environments, whether black lava or light sand, owing to adaptive mutations in the melanocortin 1 receptor and other melanin pathway genes. Physiological resistance to the heart poisons (cardiac glycosides) that monarch butterflies store in their bodies to protect themselves from predators are driven by adaptive mutations in the target of the poison, the sodium pump, resulting in target site insensitivity. These same adaptive mutations and similar changes at the same amino acid sites were found to evolve in a parallel manner in distantly related insects that feed on the same plants, and even in a bird that feeds on monarchs through convergent evolution, a hallmark of adaptation.Convergence at the gene-level across distantly related species can arise because of evolutionary constraint.

Habitats and biota do frequently change over time and space. Therefore, it follows that the process of adaptation is never fully complete. Over time, it may happen that the environment changes little, and the species comes to fit its surroundings better and better, resulting in stabilizing selection. On the other hand, it may happen that changes in the environment occur suddenly, and then the species becomes less and less well adapted. The only way for it to climb back up that fitness peak is via the introduction of new genetic variation for natural selection to act upon. Seen like this, adaptation is a genetic tracking process, which goes on all the time to some extent, but especially when the population cannot or does not move to another, less hostile area. Given enough genetic change, as well as specific demographic conditions, an adaptation may be enough to bring a population back from the brink of extinction in a process called evolutionary rescue. Adaptation does affect, to some extent, every species in a particular ecosystem.

Leigh Van Valen thought that even in a stable environment, because of antagonistic species interactions and limited resources, a species must constantly had to adapt to maintain its relative standing. This became known as the Red Queen hypothesis, as seen in host-parasite interactions.

Existing genetic variation and mutation were the traditional sources of material on which natural selection could act. In addition, horizontal gene transfer is possible between organisms in different species, using mechanisms as varied as gene cassettes, plasmids, transposons and viruses such as bacteriophages.

Co-adaptation

Pollinating insects are co-adapted with flowering plants.

In coevolution, where the existence of one species is tightly bound up with the life of another species, new or 'improved' adaptations which occur in one species are often followed by the appearance and spread of corresponding features in the other species. In other words, each species triggers reciprocal natural selection in the other. These co-adaptational relationships are intrinsically dynamic, and may continue on a trajectory for millions of years, as has occurred in the relationship between flowering plants and pollinating insects.

Mimicry

Images A and B show real wasps; the others show Batesian mimics: three hoverflies and one beetle.

Bates' work on Amazonian butterflies led him to develop the first scientific account of mimicry, especially the kind of mimicry which bears his name: Batesian mimicry. This is the mimicry by a palatable species of an unpalatable or noxious species (the model), gaining a selective advantage as predators avoid the model and therefore also the mimic. Mimicry is thus an anti-predator adaptation. A common example seen in temperate gardens is the hoverfly (Syrphidae), many of which—though bearing no sting—mimic the warning coloration of aculeate Hymenoptera (wasps and bees). Such mimicry does not need to be perfect to improve the survival of the palatable species.

Bates, Wallace and Fritz Müller believed that Batesian and Müllerian mimicry provided evidence for the action of natural selection, a view which is now standard amongst biologists.

Trade-offs

All adaptations have a downside: horse legs are great for running on grass, but they cannot scratch their backs; mammals' hair helps temperature, but offers a niche for ectoparasites; the only flying penguins do is under water. Adaptations serving different functions may be mutually destructive. Compromise and makeshift occur widely, not perfection. Selection pressures pull in different directions, and the adaptation that results is some kind of compromise.

It is a profound truth that Nature does not know best; that genetical evolution... is a story of waste, makeshift, compromise and blunder.

— Peter Medawar, The Future of Man

Since the phenotype as a whole is the target of selection, it is impossible to improve simultaneously all aspects of the phenotype to the same degree.

Examples

Consider the antlers of the Irish elk, (often supposed to be far too large; in deer antler size has an allometric relationship to body size). Antlers serve positively for defence against predators, and to score victories in the annual rut. But they are costly in terms of resources. Their size during the last glacial period presumably depended on the relative gain and loss of reproductive capacity in the population of elks during that time. As another example, camouflage to avoid detection is destroyed when vivid coloration is displayed at mating time. Here the risk to life is counterbalanced by the necessity for reproduction.

Stream-dwelling salamanders, such as Caucasian salamander or Gold-striped salamander have very slender, long bodies, perfectly adapted to life at the banks of fast small rivers and mountain brooks. Elongated body protects their larvae from being washed out by current. However, elongated body increases risk of desiccation and decreases dispersal ability of the salamanders; it also negatively affects their fecundity. As a result, fire salamander, less perfectly adapted to the mountain brook habitats, is in general more successful, have a higher fecundity and broader geographic range.

The peacock's ornamental train (grown anew in time for each mating season) is a famous adaptation. It must reduce his maneuverability and flight, and is hugely conspicuous; also, its growth costs food resources. Darwin's explanation of its advantage was in terms of sexual selection: "This depends on the advantage which certain individuals have over other individuals of the same sex and species, in exclusive relation to reproduction." The kind of sexual selection represented by the peacock is called 'mate choice,' with an implication that the process selects the more fit over the less fit, and so has survival value. The recognition of sexual selection was for a long time in abeyance, but has been rehabilitated.

The conflict between the size of the human foetal brain at birth, (which cannot be larger than about 400 cm3, else it will not get through the mother's pelvis) and the size needed for an adult brain (about 1400 cm3), means the brain of a newborn child is quite immature. The most vital things in human life (locomotion, speech) just have to wait while the brain grows and matures. That is the result of the birth compromise. Much of the problem comes from our upright bipedal stance, without which our pelvis could be shaped more suitably for birth. Neanderthals had a similar problem.

As another example, the long neck of a giraffe brings benefits but at a cost. The neck of a giraffe can be up to 2 m (6 ft 7 in) in length. The benefits are that it can be used for inter-species competition or for foraging on tall trees where shorter herbivores cannot reach. The cost is that a long neck is heavy and adds to the animal's body mass, requiring additional energy to build the neck and to carry its weight around.

Shifts in function

Adaptation and function are two aspects of one problem.

— Julian Huxley, Evolution: The Modern Synthesis

Pre-adaptation

Pre-adaptation occurs when a population has characteristics which by chance are suited for a set of conditions not previously experienced. For example, the polyploid cordgrass Spartina townsendii is better adapted than either of its parent species to their own habitat of saline marsh and mud-flats. Among domestic animals, the White Leghorn chicken is markedly more resistant to vitamin B1 deficiency than other breeds; on a plentiful diet this makes no difference, but on a restricted diet this preadaptation could be decisive.

Pre-adaptation may arise because a natural population carries a huge quantity of genetic variability. In diploid eukaryotes, this is a consequence of the system of sexual reproduction, where mutant alleles get partially shielded, for example, by genetic dominance. Microorganisms, with their huge populations, also carry a great deal of genetic variability. The first experimental evidence of the pre-adaptive nature of genetic variants in microorganisms was provided by Salvador Luria and Max Delbrück who developed the Fluctuation Test, a method to show the random fluctuation of pre-existing genetic changes that conferred resistance to bacteriophages in Escherichia coli. The word is controversial because it is teleological and the entire concept of natural selection depends on the presence of genetic variation, regardless of the population size of a species in question.

Co-option of existing traits: exaptation

The feathers of dinosaur Sinosauropteryx, were used for insulation or display, making them an exaptation for flight.

Features that now appear as adaptations sometimes arose by co-option of existing traits, evolved for some other purpose. The classic example is the ear ossicles of mammals, which we know from paleontological and embryological evidence originated in the upper and lower jaws and the hyoid bone of their synapsid ancestors, and further back still were part of the gill arches of early fish. The word exaptation was coined to cover these common evolutionary shifts in function. The flight feathers of birds evolved from the much earlier feathers of dinosaurs, which might have been used for insulation or for display.

Niche construction

Animals including earthworms, beavers and humans use some of their adaptations to modify their surroundings, so as to maximize their chances of surviving and reproducing. Beavers create dams and lodges, changing the ecosystems of the valleys around them. Earthworms, as Darwin noted, improve the topsoil in which they live by incorporating organic matter. Humans have constructed extensive civilizations with cities in environments as varied as the Arctic and hot deserts. In all three cases, the construction and maintenance of ecological niches helps drive the continued selection of the genes of these animals, in an environment that the animals have modified.

Non-adaptive traits

Some traits do not appear to be adaptive as they have a neutral or deleterious effect on fitness in the current environment. Because genes often have pleiotropic effects, not all traits may be functional: they may be what Stephen Jay Gould and Richard Lewontin called spandrels, features brought about by neighbouring adaptations, on the analogy with the often highly decorated triangular areas between pairs of arches in architecture, which began as functionless features.

Another possibility is that a trait may have been adaptive at some point in an organism's evolutionary history, but a change in habitats caused what used to be an adaptation to become unnecessary or even maladapted. Such adaptations are termed vestigial. Many organisms have vestigial organs, which are the remnants of fully functional structures in their ancestors. As a result of changes in lifestyle the organs became redundant, and are either not functional or reduced in functionality. Since any structure represents some kind of cost to the general economy of the body, an advantage may accrue from their elimination once they are not functional. Examples: wisdom teeth in humans; the loss of pigment and functional eyes in cave fauna; the loss of structure in endoparasites.

Extinction and coextinction

If a population cannot move or change sufficiently to preserve its long-term viability, then it will become extinct, at least in that locale. The species may or may not survive in other locales. Species extinction occurs when the death rate over the entire species exceeds the birth rate for a long enough period for the species to disappear. It was an observation of Van Valen that groups of species tend to have a characteristic and fairly regular rate of extinction.

Just as there is co-adaptation, there is also coextinction, the loss of a species due to the extinction of another with which it is coadapted, as with the extinction of a parasitic insect following the loss of its host, or when a flowering plant loses its pollinator, or when a food chain is disrupted.

Origin of adaptive capacities

The first stage in the evolution of life on earth is often hypothesized to be the RNA world in which short self-replicating RNA molecules proliferated before the evolution of DNA and proteins. By this hypothesis, life started when RNA chains began to self-replicate, initiating the three mechanisms of Darwinian selection: heritability, variation of type, and competition for resources. The fitness of an RNA replicator (its per capita rate of increase) would likely have been a function of its intrinsic adaptive capacities, determined by its nucleotide sequence, and the availability of resources. The three primary adaptive capacities may have been: (1) replication with moderate fidelity, giving rise to heritability while allowing variation of type, (2) resistance to decay, and (3) acquisition of resources. These adaptive capacities would have been determined by the folded configurations of the RNA replicators resulting from their nucleotide sequences.

Philosophical issues

"Behaviour with a purpose": a young springbok stotting. A biologist might argue that this has the function of signalling to predators, helping the springbok to survive and allowing it to reproduce.

Adaptation raises philosophical issues concerning how biologists speak of function and purpose, as this carries implications of evolutionary history – that a feature evolved by natural selection for a specific reason – and potentially of supernatural intervention – that features and organisms exist because of a deity's conscious intentions. In his biology, Aristotle introduced teleology to describe the adaptedness of organisms, but without accepting the supernatural intention built into Plato's thinking, which Aristotle rejected. Modern biologists continue to face the same difficulty. On the one hand, adaptation is purposeful: natural selection chooses what works and eliminates what does not. On the other hand, biologists by and large reject conscious purpose in evolution. The dilemma gave rise to a famous joke by the evolutionary biologist Haldane: "Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public.'" David Hull commented that Haldane's mistress "has become a lawfully wedded wife. Biologists no longer feel obligated to apologize for their use of teleological language; they flaunt it." Ernst Mayr stated that "adaptedness... is an a posteriori result rather than an a priori goal-seeking", meaning that the question of whether something is an adaptation can only be determined after the event.

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