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Glossary of terms


Evolution means change over time. It describes the capacity of organisms to undergo changes in their genes (genotype) and observable characteristics (phenotype) that can be a result of natural selection or genetic drift. Besides Darwin’s insight that organisms evolve by natural selection, he also realized that all organisms evolved from a common ancestor (common descent).


Fitness, sometimes also called Darwinian fitness, is a measure of the relative expected contribution of a genotype (or phenotype) to future generations. Fitness can be thought of as the number of offspring, or copies of an individual’s genes, that are left in the next generation. Fitness is the lifetime reproductive success of a genotype (or phenotype) relative to other such types in a population.


Adaptation is the process by which an organism becomes more “fit” to its environment – in other words, better able to live and reproduce in the conditions it is in. For a bacterium causing a urinary tract infection, for instance, an adaptation might be the ability to avoid destruction by the immune system or being able to survive in the presence of antibiotics.

Natural Selection

Natural selection is the motor of evolution. Natural selection results in complexity and adaptation. For natural selection to happen, you need to have variability in a trait, you need to inherit the trait (it has to have a heritable, genetic basis), the trait must have an effect on fitness (survival and reproduction) and you need sufficient time. See also:

Genetic Drift

Genetic drift is a random evolutionary change, underpinned by genetic change that is random. This is in distinction with evolution that happens by natural selection, a process that is non-random. Selection tends to produce evolutionary change that makes an organism better adapted to its environment. Drift does not. Read more here.

Founder Effect

One concept that is related to drift is the founder effect, which explains why rare alleles can exist in populations that started off with just a few individuals, when one or some of those founding individuals just happened randomly to have a copy of that rare allele. Some of these alleles that have their origin in the founder effect may increase disease risk. Another related concept, population bottlenecks, in combination with the founder effect, might explain several genetic diseases. One possible example: Tay Sachs disease is common in Ashkenazi Jews, likely because of a founder effect.

Antagonistic Pleiotropy

Pleiotropy means that a gene has more than one effect. Antagonistic pleiotropy means that a gene (or combination of genes) has more than one effect and those effects go in opposite directions. George Williams proposed this idea to explain aging – natural selection is expected to favor genes that have early life benefits – and also have late life harmful effects. In this hypothesis, aging evolved as a maladaptive byproduct of natural selection for increased fitness early in life; but these beneficial early life effects come with the cost of deleterious late life effects responsible for aging. Antagonistic pleiotropy may be ubiquitous in our genomes.

Disposable Soma Hypothesis

The disposable soma hypothesis recognizes that the non-reproductive part of the body (the soma) exists only to support the reproductive part of the body. Put simply, after successful reproduction, the soma is “disposable”, and genes are passed on. At any moment in time, an adult can devote energy to the maintenance of the body or to reproduction. This tradeoff is vividly illustrated in adult salmon, which appear to do all their aging at once, immediately after a single reproductive effort. In many animals, bearing offspring shortens lifespan. There is some evidence of this in humans too. Read more here.

Gene-Environment Mismatch

This is the idea that our genes evolved in an environment that is very different from the environment we modern people find ourselves in. So, there can be a mismatch between the environment our genes evolved to expect and the new changed environment. As a result, genes that would encode adaptations to an ancestral environment might cause disease in the modern context.

Kin Selection

Kin selection is a mechanism by which traits that benefit close relatives (increase the fitness of the individual’s relatives) proliferate by natural selection. This idea was initially put forward to explain altruism – cooperative behavior that comes at a cost to the individual – and was proposed by W. D. Hamilton. It works mathematically and in real life. Because related individuals share genes, a child that helps its parents raise siblings has increased inclusive fitness (see below). Helping relatives reproduce is favored by kin selection. Kin selection also explains grandparent interest in helping raise grandchildren and may help explain human menopause.

Inclusive Fitness

Inclusive fitness is related to kin selection. It is the concept that your relatives contribute to your fitness, e.g they contribute to the total number of your gene copies that make it into subsequent generations. Inclusive fitness relies on the idea that your close relatives share your genes (one’s parents, brothers and sisters and offspring share 50% of their genes with you, on average; aunts, uncles, and grandparents share 25%; cousins share 12.5%, and so on). Thus, individuals who help their parents raise siblings can increase their inclusive fitness and those helping behaviors can be favored by kin selection.

Proximate versus Ultimate

These are levels of analysis that can explain why things are the way they are, both in biology and in medicine. Proximate explanations are mechanistic, reductionist explanations of traits – this is what you learn mostly in medical school. Ultimate explanations are evolutionary explanations for why a trait evolved. The key to making the distinction between proximate and ultimate causation in medicine to examine how the explanation is presented. If the explanation is descriptive, takes a reductionist approach, and seeks underlying mechanisms, it is likely a proximate explanation. If the explanation invokes evolutionary history, explains things in terms of reproductive success or changes in gene frequencies, or proposes a unappreciated benefit for genes that also cause disease, it is likely an ultimate explanation. See also: Proximate and Ultimate Dichotomy in Medicine.

Balancing Selection

For some traits, negative selection is balanced by positive selection, depending on how the gene is inherited and on certain environmental features. Sickle cell trait is an example. Sickle cell trait is an extremely common blood polymorphism that has high frequency in sub-Saharan Africa. If the allele responsible for sickle cell is inherited with two copies (homozygotes) it can cause sickle cell disease, a painful hemoglobin disorder that causes red cell sludging in the microcirculation, life threatening tissue hypoxia and ischemia. Many victims of sickle cell disease die before they have children themselves. However, when a single copy of the sickle cell allele is inherited (heterozygotes), carriers are partially protected from Falciparum malaria. From the gene’s perspective, the benefit of sickle cell trait (heterozygote advantage) is counterbalanced by the lethal harm of having sickle cell disease as a homozygote. In places with endemic malaria, balancing selection explains why sickle cell alleles exist at high frequency.

Red Queen Hypothesis

The Red Queen hypothesis is named after the character from Lewis Carroll’s “Through the Looking Glass.” The Red Queen in Alice in Wonderland says “it takes all the running you can do, to keep in the same place.” In evolutionary terms, the Red Queen effect refers to the fact that we are engaged in a continuing arms race with harmful microorganisms. Each side evolves adaptations and counter-adaptions in a never ending competition. Like the Red Queen in the story, the non-stop evolution on both sides means that neither host nor pathogen has the upper hand for long, so both competitors stay in roughly the same “place.”

Hygiene Hypothesis

The hygiene hypothesis is an explanation for the recent increase in asthma, autoimmune, and allergy diagnoses in the last half-century. The hygiene hypothesis was proposed by Bach in 2002, who noted an inverse relationship between family size and allergic diseases and suggested that childhood infections have a protective effect for allergy. Also termed the “old friends” hypothesis, it contends that increases in autoimmune inflammatory disorders in developed countries are partly attributable to decreasing exposure to microorganisms with which humans coevolved. (Excerpted from Alcock and Schwartz 2012).

Life History Theory

Life History Theory, a concept first put forward by Yale evolutionary biologist Stephen Stearns, is the application of evolutionary biology to the entire life cycle from birth to death. It hypothesizes that features of life are shaped by natural selection in ways that maximized fitness during our evolutionary past. These life history features include: the long (9 month) gestation period of humans, the relative helplessness and dependence on parental protection of the human infant (altriciality), our long childhood, the timing of reproductive maturity (menarche and adrenarche) and sex differences in development, body size, the timing and existence of menopause, how we age, and the timing of death. Two central ideas are needed to understand life history theory: energy constraints and tradeoffs. Organisms have access to limited energy during any given point in the life cycle and that resource constraint drives important tradeoffs. See also: LHT and the microbiome.

Host Defenses

Randolph Nesse and others proposed that many uncomfortable symptoms that make patients seek medical or psychiatric care are in fact adaptations that are protective from various life threats. Cough, diarrhea, nausea, vomiting, fever, anxiety, panic, and other symptoms have a defensive role when an organism is confronted by a pathogen or a predator. Cough expels pathogens from the lungs. Diarrhea and vomiting has a similar defensive role in the gut. Fever helps clear infection. Panic and anxiety can help individuals avoid injury or worse from predators or dangerous members of their own species. Recognizing host defenses means that these symptoms are not simply pathophysiologic signs that always should be treated by a physician in a knee-jerk response. Instead, the potential benefits of these responses should be considered along with their costs, before deciding on treatment.

Smoke Detector Principle

Randolph Nesse coined the term smoke detector principle to explain why some people display an exaggerated response to threats, perceived and real, resulting in anxiety disorders and panic. He writes: “False alarms are to be expected” because of uncertainty about the nature of a threat. That alarming noise behind you that triggers an involuntary intake of breath and a racing heart might simply be a harmless falling branch, or a charging grizzly bear. The overreaction to the falling branch evolved because hair-trigger reactions protect us from the far greater cost of being eaten alive. Beyond panic, the smoke detector principle might apply to other host defenses such as immune responses to dangerous microbes. More here.

Sickness Behaviors

Sickness behaviors are a syndrome of host defenses that are triggered when an organism is suffering infection. In mice, sickness behaviors include ruffled fur, inactivity, glazed appearance of the eyes, and not eating. Humans with sickness behavior similarly reduce eating behavior and decrease social interaction. Sickness behaviors and symptoms also include headache, nausea, along with signs such as fever, and increased acute phase proteins in the blood. The fact that these symptoms happen consistently and in a reproducible way in almost everybody , and that they also occur in many other species suggests that sickness behaviors might be adaptive in the setting of infection. Theoretic and experimental work supports this viewpoint. Read more here.

Immune Brinksmanship

Legrand and Alcock coined the term immune brinksmanship, the idea that the host undertakes a risky gamble when mounting an immune response against infection. The gamble is that the response involves costs and harms to both the host and the pathogen. The host gambles that those harms will be disproportionately borne by the pathogen. The analogy is one of trade sanctions in which a country might undertake an economically-injurious cessation of trade with a competitor, with the calculation that the competitor will bear the brunt of the economic injury. The prescription of cancer chemotherapy uses the same logic. Selection acting on hosts is expected to minimize, but not eliminate, the costs suffered by hosts from an immune response, are so that the odds of success are in the house’s favor, like a casino. More here.

Predictive Adaptive Response

The notion that early life experiences, including nutrient transfer from the mother in utero, can anticipate future environments and also shape the risk of later adult diseases has been termed the predictive adaptive response, or PAR. The PAR builds on the observation that many organisms, including humans, have developmental plasticity. Exposures early in life can shape our bodies and our risk for disease, particularly our growth rate, the risk of adult obesity, heart disease, and diabetes (see DOHad below). Researchers have proposed that some of these developmental changes might be adaptive if early life exposures predict the state of the future environment that an organisms will live in. The PAR is an important idea in evolutionary medicine, but it is controversial. Read more here.

DOHaD and Thrifty Phenotype Hypothesis

The Developmental Origin of Health and Disease (DOHaD) concept first came to light when Barker documented a curious association between birth weight and adult cardiac events in British men. Babies born small had a higher risk of chronic inflammatory diseases as adults. These small babies have been described as adopting a “thrifty phenotype.” That is, nutrient deprivation as a fetus is thought to have shaped the developmental trajectory in these individuals. The change includes reduced expenditure on muscle and increased energy storage as fat. These “thrifty phenotype” adjustments are “thrifty” because muscle uses much greater metabolic fuel than does fat. Metabolic thriftiness, along with less energy used by costly muscle tissue, and increased ability to mobilize energy during times of stress are hypothesized to be adaptations that promote survival. In terms of human development, the thrifty phenotype also preserves priority energy access for key organs, such as the brain.  For more, read Kuzawa et al: Developmental Origins of Adult Function and Health: Evolutionary Hypotheses.

Imprinting – Parent of Origin Effects

Gene imprinting or genomic imprinting results in genes being expressed differently depending on which parent the gene copy is inherited from. About 10-20% of genes show an imprinting effect, meaning that a gene might be turned on, or turned off, depending on which parent it comes from. from. This parent-of-origin imprinting effect is an extension of parent offspring conflict, first developed by Robert Trivers. Parent offspring conflict is an expected outcome of the fact that parents and offspring do not share 100% of genes. As a result, the fitness interests of offspring do not align perfectly with the interests of each parent. Imprinting often has functional consequences that serve the different fitness interests of mom and dad. More specifically, imprinting represents genetic conflict between the chunk of the baby’s genome that overlaps with the mom’s genome and the chunk of baby’s genome that overlaps with dad’s genome. This is slightly complicated, but understandable only in light of evolution!

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