Evolutionary Adaptations Flashcards
Evolvability
- the capacity of a system for adaptive evolution
- the ability of a population of organisms to generate adaptive genetic diversity, and thereby evolve through natural selection.
Exaptation
a shift in the function of a trait during evolution
teleologically
loaded
co-option
- the capacity of intracellular parasites to use host-cell proteins to complete their vital cycle
- Viruses use this mechanism, as their genome is small
- characters that have been exapted
Obligate altruism
- the permanent loss of direct fitness (with potential for indirect fitness gain).
- honey bee workers may forage for the colony.
Facultative altruism
- temporary loss of direct fitness (with potential for indirect fitness gain followed by personal reproduction). - Florida scrub jay may help at the nest, then gain parental territory.
binocular vision basics
- animal has two eyes capable of facing the same direction to perceive a single three-dimensional image of its surroundings.
binocular vision specifics
- “spare eye” in case one is damaged.
- wider field of view.
- stereopsis in which binocular disparity (or parallax) provided by the two eyes’ different positions on the head gives precise depth perception. This also allows a creature to break the camouflage of another creature.
- allows the angles of the eyes’ lines of sight, relative to each other (vergence), and those lines relative to a particular object (gaze angle) to be determined from the images in the two eyes.
- allows a creature to see more of, or all of, an object behind an obstacle.
- binocular summation in which the ability to detect faint objects is enhanced.
binocular vision in humans
- humans have a maximum horizontal field of view of approximately 190 degrees with two eyes
- approximately 120 degrees makes up the binocular field of view
- flanked by two uniocular fields (seen by only one eye) of approximately 40 degrees.
Kin selection
- the evolutionary strategy that favours the reproductive success of an organism’s relatives, even at a cost to the organism’s own survival and reproduction.
- an instance of inclusive fitness, which combines the number of offspring produced with the number an individual can ensure the production of by supporting others, such as siblings.
Example of kin selection
eusocial sterile insects
kin recognition allows
individuals to be able to identify their relatives.
in viscous populations
- local interactions tend to be among relatives by default
- makes kin selection and social cooperation possible in the absence of kin recognition; nurture kinship
viscous populations
- populations in which the movement of organisms from their place of birth is relatively slow
- give reasonable assumptions about population dispersal rates
- organisms interacting in their natal context
- without active kin discrimination, since social participants by default typically share recent common origin
nurture kinship
- the treatment of individuals as kin as a result of living together
- cue-based and context-based mechanisms, such as familiarity, imprinting and phenotype matching.
allomothering
related females such as older sisters or grandmothers often care for young, according to their relatedness.
Kin recognition (kin detection)
- an organism’s ability to distinguish between close genetic kin and non-kin
- evolved for inbreeding avoidance
cue-based ‘recognition’
- predominates in social mammals
- outcomes are non-deterministic in relation to actual genetic kinship, instead outcomes simply reliably correlate with genetic kinship in an organism’s typical conditions
imprinting
phase-sensitive learning that is rapid and apparently independent of the consequences of behaviour.
phase-sensitive learning
learning occurring at a particular age or a particular life stage
critical period
a maturational stage in the lifespan of an organism during which the nervous system is especially sensitive to certain environmental stimuli.
Westermarck effect (reverse sexual imprinting)
a psychological hypothesis that people tend not to be attracted to peers with whom they lived like siblings before age six.
altruism
behaviour by an individual that increases the fitness of another individual while decreasing the fitness of the actor
Brood parasites
- organisms that rely on others to raise their young
- often achieved by egg mimicry
egg mimicry
- having eggs that resemble the host’s
- very strong rejection defenses resulting in the parasitic species evolving to have very close mimicry.
- In other species, hosts do not show rejection defenses and as a result, the parasitic species will show no evolved trait
Sociality
- gregariousness
- formation of cooperative societies
- a survival response to evolutionary pressures
Gregariousness
the degree to which individuals in an animal population tend to associate in social groups
Parental investment
detracts from a parent’s capacity to invest in future reproduction and aid to kin (including other offspring).
subsocial
An animal that cares for its young but shows no other sociality traits
social animal
An animal that exhibits a high degree of sociality
eusocial taxa
- exhibits overlapping adult generations
- reproductive division of labor
- cooperative care of young
- a biological caste system.
Group selection
- a proposed mechanism of evolution in which natural selection acts at the level of the group (not individual)
- multi-level selection
- groups, like individuals, could compete
- strong rebuttal from a large group of evolutionary biologists and behavior analysts
group selection could occur when
competition between two or more groups, some containing altruistic individuals who act cooperatively together, is more important for survival than competition between individuals within each group
selfish gene theory
- adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation
- evolutionary success ultimately depends on leaving behind the maximum number of copies of itself in the population
Distraction displays (diversionary displays/paratrepsis)
- anti-predator behaviors used to attract the attention of an enemy away from something, typically the nest or young, that is being protected by a parent.
- classified more generically under “nest protection behaviors” along with aggressive displays such as mobbing.
selfish herd theory basics
- individuals within a population attempt to reduce their predation risk by putting other conspecifics between themselves and predators
- results from the domain of danger
- results in aggregations
the domain of danger
the area of ground in which every point is nearer to a particular individual than to any other individual
selfish herd theory specifics
- in aggregations, predation risk is greatest on the periphery and decreases toward the center.
- more dominant animals within the population are proposed to obtain low-risk central positions, whereas subordinate animals are forced into higher risk positions.
what does the selfish herd theory explain
- why populations at higher predation risk often form larger, more compact groups.
- why these aggregations are often sorted by phenotypic characteristics such as strength.
Mobbing
- an antipredator adaptation
- an assemblage of individuals around a potentially dangerous predator
- individuals of prey species mob a predator by cooperatively attacking or harassing it, usually to protect their offspring
Intragenomic conflict
the evolutionary phenomenon where genes have phenotypic effects that promote their own transmission in detriment of the transmission of other genes that reside in the same genome
coefficient of relationship
a measure of the degree of consanguinity between two individuals
consanguinity
- biological relationship
- the characteristic of having a kinship with another person
- being descended from a common ancestor
ahnentafel
- a genealogical numbering system for listing a person’s direct ancestors in a fixed sequence of ascent.
- proband is listed as No. 1, the subject’s father as No. 2 and the mother as No. 3
- (exc. 1) all even-numbered persons are male, and all odd-numbered persons are female
- the number of any person’s father is double the person’s number, and a person’s mother is double the person’s number plus one.
proband
subject
Fictive kinship
- forms of kinship or social ties that are based on neither consanguineal nor affinal ties
- contrasts with true kinship ties.
affinal
(“by marriage”)
the expression of social behavior may be mediated by
correlated conditions, such as:
- shared location
- shared rearing environment
- familiarity or other contextual cues which correlate with shared genetic relatedness
Ethnocentrism
to apply one’s own culture or ethnicity as a frame of reference to judge other cultures, practices, behaviors, beliefs, and people, instead of using the standards of the particular culture involved.
inclusive fitness theory
- the number of offspring equivalents that an individual rears, rescues or otherwise supports through its behaviour (regardless of who begets them)
mathematical basis of the inclusive fitness theory
- an individual’s own child, who carries one half of the individual’s genes, is defined as one offspring equivalent.
- a sibling’s child, who will carry one-quarter of the individual’s genes, is 1/2 offspring equivalent
- a cousin’s child, who has 1/16 of the individual’s genes, is 1/8 offspring equivalent.
Green-beard hypothesis
- whereas kin selection involves altruism to related individuals who share genes in a non-specific way, green-beard alleles promote altruism toward individuals who share a gene that is expressed by a specific phenotypic trait.
Green-beard alleles
vulnerable to mutations that produce the perceptible trait without the helping behaviour.
Why are green-beard alleles necessary?
A gene for (behavioral) selective altruism can be favored by natural selection if the altruism is primarily directed at other individuals who share the gene. Since genes are invisible, such an effect requires perceptible markers for altruistic behaviour to occur.
Haplodiploidy
a sex-determination system in which males develop from unfertilized eggs and are haploid, and females develop from fertilized eggs and are diploid
Particulate inheritance
phenotypic traits can be passed from generation to generation through “discrete particles” (genes), which can keep their ability to be expressed while not always appearing in a descending generation
Law of Use and Disuse
- if you choose to use a body part often, it will develop. If you choose not to use it, it will get smaller and disappear
- essentially, features are accentuated or attenuated
Law of Inheritance of Acquired Characteristics (soft inheritance)
changes resulting from the law of use and disuse will happen in your own lifetime, and they will become part of your body plan. Your sperm/ovum will pass it on to your children.
Incongruities with Lamarckian inheritance
- often stretching your own neck will not give you a longer neck.
- children of de-tailed rats were still born with tails
Pangenesis theory
the idea that somatic cells would, in response to environmental stimulation (use and disuse), throw off ‘gemmules’ or ‘pangenes’ which travelled around the body, though not necessarily in the bloodstream.
Pangenes
- microscopic particles that supposedly contained information about the characteristics of their parent cell
- Darwin believed that they eventually accumulated in the germ cells where they could pass on to the next generation the newly acquired characteristics of the parents
Law of Dominance and Uniformity
dominant alleles, and the uniformity of the F1 generation in heterozygosity
intermediate inheritance
incomplete dominance
Law of Segregation (The Law of Independent Assortment)
– in F2 population
- alleles for separate traits are passed independently of one another. (shown by (9:3:3:1)
- In cases of codominance the phenotypes produced by both alleles are clearly expressed
Lamarckian methylation and chromatin marks (on histones)
- involved in gene regulation
- marks are responsive to environmental stimuli, differentially affect gene expression, and are adaptive, with phenotypic effects that persist for some generations.
- e.g. Dutch Hunger Winter
- Jablonka and Lamb pro
- Thomas Dickens and Qazi Rahman (2012) against
Lamarckian CRISPR
CRISPR arrays can be passed onto offspring – in an acquired genetic immunity.
evolutionary landscape basics
- used to visualise the processes of evolution (e.g. natural selection and genetic drift) acting on a biological entity (e.g. a gene, protein, population, or species).
evolutionary landscape specifics
- entity can be viewed as searching or moving through a search space. For example, the search space of a gene would be all possible nucleotide sequences.
- “y-axis”: usually fitness.
- If small movements through search space cause changes in fitness that are relatively small, then the landscape is considered smooth.
- In contrast, if small movements result in large changes in fitness, then the landscape is said to be rugged.
- In either case, movement tends to be toward areas of higher fitness, though usually not the global optima.
Smooth evolutionary landscapes
happen when most fixed mutations have little to no effect on fitness, which is what one would expect with the neutral theory of molecular evolution.
Epistasis
- phenomenon in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes (modifier genes)
- the effect of the mutation is dependent on the genetic background in which it appears.
- Epistatic mutations therefore have different effects on their own than when they occur together.
Epigenetics
- epigenetic inheritance lasts for only a few generations, so it is not a stable basis for evolutionary change
- evolution of epigenetic switches by natural selection
Orthogenesis (orthogenetic evolution/progressive evolution/evolutionary progress/ progressionism)
- the biological hypothesis that organisms have an innate tendency to evolve in a definite direction towards some goal (teleology) due to some internal mechanism or “driving force”.
- the largest-scale trends in evolution have an absolute goal such as increasing biological complexity.
Lamarckian inheritance is an example of
orthogenesis
The modern synthesis
the early 20th-century synthesis reconciling Charles Darwin’s theory of evolution and Gregor Mendel’s ideas on heredity in a joint mathematical framework.
The Hardy–Weinberg principle provides
- the solution to how variation is maintained in a population with Mendelian inheritance.
- the frequencies of alleles will remain constant in the absence of selection, mutation, migration and genetic drift.
Fisher showed that
natural selection could change allele frequencies in a population, resulting in evolution.
Quantitative genetics deals with
phenotypes that vary continuously
gamodeme
a breeding population
Population genetics vs qualitative genetics
While population genetics can focus on particular genes and their subsequent metabolic products, quantitative genetics focuses more on the outward phenotypes, and makes summaries only of the underlying genetics.
Molecular genetics
- a sub-field of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms.
- often applies an “investigative approach” to determine the structure and/or function of genes in an organism’s genome using genetic screens.
Genetic linkage
- the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction.
- two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart.
- markers on different chromosomes are perfectly unlinked.
Genetic linkage is the most prominent exception to
Gregor Mendel’s Law of Independent Assortment.
genetic marker
- a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species.
- variation (which may arise due to mutation or alteration in the genomic loci) that can be observed – e.g. minisatellites, microsatellites, short tandem variable repeats, variable number of tandem repeats
Population genomics
- the large-scale comparison of DNA sequences of populations.
- to study rapid adaptive evolution
- integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked.
The main processes influencing allele frequencies are
natural selection, genetic drift, gene flow and recurrent mutation.
Gene duplications
- arise as products of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements.
- ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.
Non-homologous end joining (NHEJ) - the basics
- a pathway that repairs double-strand breaks in DNA.
- the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair, which requires a homologous sequence to guide repair.
NHEJ - the specifics
- typically guided by short homologous DNA sequences called microhomologies (often present in single-stranded overhangs on the ends of double-strand breaks).
- when the overhangs are perfectly compatible, NHEJ usually repairs the break accurately.
- imprecise repair leading to loss of nucleotides can also occur, but is much more common when the overhangs are not compatible.
- inappropriate NHEJ can lead to translocations and telomere fusion, hallmarks of tumor cells
DNA mismatch repair (MMR)
a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.
nick
a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand, typically through damage or enzyme action
- allow DNA strands to untwist during replication
- thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands
Base excision repair (BER) - the theory
- a cellular mechanism that repairs damaged DNA throughout the cell cycle.
- responsible primarily for removing small, non-helix-distorting base lesions from the genome.
- important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication.
BER - the process
- initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites.
- cleaved by an AP endonuclease.
- resulting single-strand break can then be processed by either short-patch (where a single nucleotide is replaced) or long-patch BER (where 2–10 new nucleotides are synthesised).
AP site (apurinic/apyrimidinic site), aka an abasic site
a location in DNA that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage.
Ectopic recombination
- an atypical form of recombination in which crossing over occurs at non-homologous, rather than along homologous, loci
- often results in dramatic chromosomal rearrangement, which is generally harmful to the organism
Transposable elements
repetitious sequences of DNA that can insert themselves into any part of the genome
Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates)
a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the process reverse transcription using an RNA transposition intermediate.
transposons vs retrotransposons
retrotransposons can be thought of as replicative, whereas DNA transposons are non-replicative.
Slipped strand mispairing (SSM), (also known as replication slippage)
- a mutation process which occurs during DNA replication.
- denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases.
- one explanation for the origin and evolution of repetitive DNA sequences.
- when DNA polymerase encounters a direct repeat, it can undergo a replication slippage – tandem repeats are unstable
Evolutionary game theory:
- it is ultimately genes that play out a full contest
- the contesting genes are present in an individual and to a degree in all of the individual’s kin.
- this can sometimes profoundly affect which strategies survive, especially with issues of cooperation and defection.
Population dynamics
the type of mathematics used to model and study the size and age composition of populations as dynamical systems.
Evolutionary dynamics
the study of the mathematical principles according to which biological organisms as well as cultural ideas evolve and evolved
Weak selection
- when individuals with different phenotypes possess similar fitness, i.e. one phenotype is weakly preferred over the other.
- an evolutionary theory to explain the maintenance of multiple phenotypes in a stable population.
- can only be used to explain the maintenance of mutations in a Moran process.
- two phenotypes with similar fixation probabilities.
- elongates fixation time for two competing alleles.
- sensitive to the effects of population size.
Moran process
birth and death are paired events, and therefore population size remains constant.
neutral theory of molecular evolution
- most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to genetic drift of mutant alleles that are selectively neutral.
- allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level.
- because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage
gene flow (gene migration/geneflow/allele flow) - the basics
- the transfer of genetic material from one population to another.
- if the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be considered a single effective population- reduces the genetic differentiation between the two groups, increasing homogeneity.
- constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaption
- it takes only “one migrant per generation” to prevent populations from diverging due to drift.
- an important mechanism for transferring genetic diversity among populations.
Why do populations diverge?
- populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough.
adaptive introgression
dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population