Evolutionary Adaptations Flashcards
(268 cards)
1
Q
Evolvability
A
- 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.
2
Q
Exaptation
A
a shift in the function of a trait during evolution
3
Q
teleologically
A
loaded
4
Q
co-option
A
- 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
5
Q
Obligate altruism
A
- the permanent loss of direct fitness (with potential for indirect fitness gain).
- honey bee workers may forage for the colony.
6
Q
Facultative altruism
A
- 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.
7
Q
binocular vision basics
A
- animal has two eyes capable of facing the same direction to perceive a single three-dimensional image of its surroundings.
8
Q
binocular vision specifics
A
- “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.
9
Q
binocular vision in humans
A
- 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.
10
Q
Kin selection
A
- 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.
11
Q
Example of kin selection
A
eusocial sterile insects
12
Q
kin recognition allows
A
individuals to be able to identify their relatives.
13
Q
in viscous populations
A
- local interactions tend to be among relatives by default
- makes kin selection and social cooperation possible in the absence of kin recognition; nurture kinship
14
Q
viscous populations
A
- 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
15
Q
nurture kinship
A
- 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.
16
Q
allomothering
A
related females such as older sisters or grandmothers often care for young, according to their relatedness.
17
Q
Kin recognition (kin detection)
A
- an organism’s ability to distinguish between close genetic kin and non-kin
- evolved for inbreeding avoidance
18
Q
cue-based ‘recognition’
A
- 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
19
Q
imprinting
A
phase-sensitive learning that is rapid and apparently independent of the consequences of behaviour.
20
Q
phase-sensitive learning
A
learning occurring at a particular age or a particular life stage
21
Q
critical period
A
a maturational stage in the lifespan of an organism during which the nervous system is especially sensitive to certain environmental stimuli.
22
Q
Westermarck effect (reverse sexual imprinting)
A
a psychological hypothesis that people tend not to be attracted to peers with whom they lived like siblings before age six.
23
Q
altruism
A
behaviour by an individual that increases the fitness of another individual while decreasing the fitness of the actor
24
Q
Brood parasites
A
- organisms that rely on others to raise their young
- often achieved by egg mimicry
25
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
26
Sociality
- gregariousness
- formation of cooperative societies
- a survival response to evolutionary pressures
27
Gregariousness
the degree to which individuals in an animal population tend to associate in social groups
28
Parental investment
detracts from a parent's capacity to invest in future reproduction and aid to kin (including other offspring).
29
subsocial
An animal that cares for its young but shows no other sociality traits
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social animal
An animal that exhibits a high degree of sociality
31
eusocial taxa
- exhibits overlapping adult generations
- reproductive division of labor
- cooperative care of young
- a biological caste system.
32
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
33
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
34
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
35
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.
36
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
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the domain of danger
the area of ground in which every point is nearer to a particular individual than to any other individual
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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.
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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.
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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
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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
42
coefficient of relationship
a measure of the degree of consanguinity between two individuals
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consanguinity
- biological relationship
- the characteristic of having a kinship with another person
- being descended from a common ancestor
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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.
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proband
subject
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Fictive kinship
- forms of kinship or social ties that are based on neither consanguineal nor affinal ties
- contrasts with true kinship ties.
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affinal
("by marriage")
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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
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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.
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inclusive fitness theory
- the number of offspring equivalents that an individual rears, rescues or otherwise supports through its behaviour (regardless of who begets them)
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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.
52
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.
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Green-beard alleles
vulnerable to mutations that produce the perceptible trait without the helping behaviour.
54
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.
55
Haplodiploidy
a sex-determination system in which males develop from unfertilized eggs and are haploid, and females develop from fertilized eggs and are diploid
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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
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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
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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.
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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
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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.
61
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
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Law of Dominance and Uniformity
dominant alleles, and the uniformity of the F1 generation in heterozygosity
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intermediate inheritance
incomplete dominance
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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
65
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
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Lamarckian CRISPR
CRISPR arrays can be passed onto offspring – in an acquired genetic immunity.
67
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).
68
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.
69
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.
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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.
71
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
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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.
73
Lamarckian inheritance is an example of
orthogenesis
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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.
75
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.
76
Fisher showed that
natural selection could change allele frequencies in a population, resulting in evolution.
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Quantitative genetics deals with
phenotypes that vary continuously
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gamodeme
a breeding population
79
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.
80
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.
81
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.
82
Genetic linkage is the most prominent exception to
Gregor Mendel's Law of Independent Assortment.
83
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
84
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.
85
The main processes influencing allele frequencies are
natural selection, genetic drift, gene flow and recurrent mutation.
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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.
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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.
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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
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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.
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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
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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.
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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).
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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.
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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
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Transposable elements
repetitious sequences of DNA that can insert themselves into any part of the genome
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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.
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transposons vs retrotransposons
retrotransposons can be thought of as replicative, whereas DNA transposons are non-replicative.
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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
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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.
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Population dynamics
the type of mathematics used to model and study the size and age composition of populations as dynamical systems.
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Evolutionary dynamics
the study of the mathematical principles according to which biological organisms as well as cultural ideas evolve and evolved
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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.
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Moran process
birth and death are paired events, and therefore population size remains constant.
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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
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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.
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Why do populations diverge?
- populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough.
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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
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when is gene flow expected to be lower?
expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there is long distances between populations, and when there are small population sizes.
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What happens when gene flow is impeded?
- increase in inbreeding, measured by the inbreeding coefficient (F) within a population. - many island populations have low rates of gene flow due to geographic isolation and small population sizes.
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Genetic drift (allelic drift or the Sewall Wright effect)[1] is
- the change in the frequency of an existing allele in a population due to random sampling of organisms.
- alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces.
- neutral process
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What does genetic drift cause?
- gene variants to disappear completely and thereby reduce genetic variation.
- initially rare alleles to become much more frequent and even fixed.
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How does the effect of genetic drift vary?
When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller.
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Sexual selection - the basics
- a mode of natural selection in which members of one biological sex choose mates of the other sex to mate with (intersexual selection), and compete with members of the same sex for access to members of the opposite sex (intrasexual selection).
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What does sexual selection cause
- some individuals have greater reproductive success than others within a population,
- successful males benefit from frequent mating and monopolizing access to one or more fertile females.
- females can have a limited number of offspring and maximize the return on the energy they invest in reproduction.
- males demonstrate their fitness to be chosen by females, producing sexual dimorphism in secondary sexual characteristics, such as the ornate plumage of birds such as birds of paradise and peafowl, or the antlers of deer, or the manes of lions
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mate
candidates
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Fischerian runaway selection:
- accounts for the evolution of exaggerated male ornamentation by persistent, directional female choice; costly ornaments.
- includes sexually dimorphic phenotypic traits such as behavior expressed by a particular sex.
- the ornament signalls greater potential fitness, so preference for the ornament had a selective advantage.
- if strong enough, female preference for exaggerated ornamentation in mate selection could be enough to undermine natural selection even when the ornament has become non-adaptive.
- over subsequent generations this could lead to runaway selection by positive feedback, and the speed with which the trait and the preference increase could (until counter-selection interferes) increase exponentially.
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Sexual antagonistic co-evolution
- the relationship between males and females where sexual morphology changes over time to counteract the opposite's sex traits to achieve the maximum reproductive success.
- e.g. traumatic insemination
- females that possess traits to avoid multiple matings will be more likely to survive, resulting in a change in morphology. - in males, genitalia is relatively simple and more likely to vary among generations compared to female genitalia. This results in a new trait that females have to avoid in order to survive.
118
The Red Queen hypothesis
- proposes that species must constantly adapt, evolve, and proliferate in order to survive while pitted against ever-evolving opposing species.
- explains the constant (age-independent) extinction probability as observed in the paleontological record caused by co-evolution between competing species
- explains the advantage of sexual reproduction at the level of individuals, and the positive correlation between speciation and extinction rates in most higher taxa.
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Blending inheritance
an obsolete theory that the progeny inherits any characteristic as the average of the parents' values of that characteristic.
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Fisher
predicted that parental expenditure on both sexes should be equal.
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Fisherian sex ratios
Sex ratios that are 1:1 are hence known as "Fisherian", and those that are not 1:1 are "non-Fisherian" or "extraordinary" and occur because they break the assumptions made in Fisher's model.
122
Vitalism
"living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things."
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complexity - how is it measured?
is very hard to define or measure accurately in biology, with properties such as gene content, the number of cell types or morphology all proposed as possible metrics
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complexity - how does it arise?
in the co-evolution of hosts and pathogens (parasites), and predators and prey- with each side developing ever more sophisticated adaptations, such as the immune system
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Why aren’t all organisms parasitic, to conserve the energy of metabolite synthesis/through genetic drift?
Depending on how you define, parasitic, we all are.
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evolutionary arms race
- a struggle between competing sets of co-evolving genes, traits, or species, that develop adaptations and counter-adaptations against each other
- an example of a positive-feedback loop
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Parental investment
- any parental expenditure (e.g. time, energy, resources) that benefits offspring.
- pre-natal (e.g. egg guarding and incubation in birds, and placental nourishment in mammals) to post-natal (e.g. food provisioning and protection of offspring).
128
parental investment theory
- predicts that the sex that invests more in its offspring will be more selective when choosing a mate, and the less-investing sex will have intra-sexual competition for access to mates.
- explains sex differences in sexual selection and mate preferences
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Ecological genetics
- the study of genetics in natural populations.
- traits (of ecological significance) in a population can be observed and quantified to represent a species adapting to a changing environment.
e. g: flowering time, drought tolerance, polymorphism, mimicry, and avoidance of attacks by predators.
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ecological significance
related to fitness
131
mimicry
- an evolved resemblance between an organism and another object, often an organism of another species.
- masquerade and mimesis.
- between different species, or between individuals of the same species.
- anti-predator adaptation.
- can be visual, acoustic, chemical, tactile, or electric, or combinations of these sensory modalities.
132
How does mimicry evolve?
if a receiver (such as a predator) perceives the similarity between a mimic (the organism that has a resemblance) and a model (the organism it resembles) and as a result changes its behaviour in a way that provides a selective advantage to the mimic
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Types of mimicry:
Mimicry may be to the advantage of both organisms that share a resemblance, in which case it is a form of mutualism; or mimicry can be to the detriment of one, making it parasitic or competitive.
134
Müllerian mimicry - the basics
- a natural phenomenon in which two or more well-defended species, often foul-tasting and that share common predators, have come to mimic each other's honest warning signals, to their mutual benefit.
- predators can learn to avoid all of them with fewer experiences with members of any one of the relevant species.
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Mullerian mimicry - the specifics
- anything that tends to deter predators, such as foul taste, sharp spines, or defensive behaviour
- unprofitable to predators
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antagonistic co-evolution through mimicry
pollinators shows that they may waste large amounts of sperm by ejaculating onto the flower; pollinators become better at identifying their own species correctly and orchids become better mimics
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Pseudocopulation
- behaviors similar to copulation that serve a reproductive function for one or both participants but do not involve actual sexual union between the individuals
- e.g. pollinator attempting to copulate with a flower.
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Pouyannian mimicry
- some flowers mimic a potential female insect mate visually, but the key stimuli are often chemical and tactile
- secreting chemicals from glands (osmophores) in the sepals, petals, or labellum, that are indistinguishable from the insect's natural pheromones.
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Mullerian mimicry - the consequences
Once a pair of Müllerian mimics has formed, other mimics may join them by advergent evolution, forming mimicry rings.
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advergent evolution
one species changing to conform to the appearance of the pair, rather than mutual convergence
141
the mathematics of mimicry
the frequency of mimics is positively correlated with survivability; rarer mimics are likely to adapt to resemble commoner models, favouring both advergence and larger Müllerian mimicry rings.
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Batesian mimicry
a harmless species has evolved to imitate the warning signals of a harmful species directed at a predator of them both.
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honest signalling
- reliably conveys useful information to the receiver.
- the signal trait tells the receiver about an otherwise unobservable factor
- can utilise any of the sensory modalities
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Aggressive mimicry is a form of mimicry in which
- predators, parasites, or parasitoids share similar signals, using a harmless model, allowing them to avoid being correctly identified by their prey or host.
- often involves the predator employing signals which draw its potential prey towards it, a strategy which allows predators to simply sit and wait for prey to come to them
145
Example of aggressive mimicry
fatal feline attraction
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Aposematism
advertising by an animal to potential predators that it is not worth attacking or eating.
147
warning
coloration
148
Deimatic behaviour (startle display)
any pattern of bluffing behaviour in an animal that lacks strong defences, such as suddenly displaying conspicuous eyespots, to scare off or momentarily distract a predator, thus giving the prey animal an opportunity to escape
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Anti-predator adaptations
- mechanisms developed through evolution that assist prey organisms in their constant struggle against predators.
- avoiding detection, warding off attack, fighting back, or escaping when caught.
150
Apostatic selection
- a form of negative frequency-dependent selection.
- survival of individual prey animals that are different (through mutation) from their species in a way that makes it more likely for them to be ignored by their predators.
- operates on polymorphic species.
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Search images
- how a predator is able to detect an organism as a possible prey
- allow apostatic selection
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Why is apostatic selection important?
It can sustain a stable equilibrium of morph frequencies, and hence maintains large amounts of genetic diversity in natural populations.
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crypsis
- the ability of an animal or a plant to avoid observation or detection by other animals.
- predation strategy or an antipredator adaptation.
- camouflage, nocturnality, subterranean lifestyle and mimicry.
- visual, olfactory (with pheromones), or auditory concealment.
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cryptic colouration
visual crypsis
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guild (in ecology)
- any group of species that exploit the same resources, or that exploit different resources in related ways.
- defined according to the locations, attributes, or activities of their component species.
- e.g. mode of acquiring nutrients, the mobility, and the habitat zones that the species occupy or exploits
- does not need to be taxonomically cohesive
- can have constituent guilds
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disparity
the number of guilds occupying an ecosystem
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Relationships within guilds
- competing for resources, such as space or light
| - cooperating in resisting wind stresses, attracting pollinators, or detecting predators
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metabolic rate
the fundamental biological rate that governs most observed patterns in ecology.
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metabolic scaling theory
- attempts to provide a unified theory for the importance of metabolism in driving pattern and process from cells to biosphere
- interpretation of the relationships between body size, body temperature, and metabolic rate across all organisms.
- small-bodied organisms tend to have higher mass-specific metabolic rates than larger-bodied organisms.
- organisms that operate at warm temperatures through endothermy or by living in warm environments tend towards higher metabolic rates than organisms that operate at colder temperatures.
- consistent from the unicellular level up to the level of the largest animals and plants on the planet.
- the primary constraint that influences biological processes (via their rates and times) at all levels of organization (from individual up to ecosystem level).
- a macroecological theory
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Macroecology
- the study of relationships between organisms and their environment at large spatial scales to characterise and explain statistical patterns of abundance, distribution and diversity
- "top down" approach
- seeks understanding through the study of the properties of the system as a whole
- how global development in climate change affect wildlife populations – species richness, abundance, diversity, distribution.
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taxocene (from Greek τάξις and κοινός)
- a taxonomically related set of species within a community
| - a group of species that belong to particular supraspecific taxon and occur together in the same association
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Trophic species
- grouping of organisms according to their shared trophic (feeding) positions in a food web or food chain. - have identical prey and a shared set of predators in the food web.
- share many of the same kinds of ecological functions.
- usually part of the same guild
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Primordium
- an organ or tissue in its earliest recognizable stage of development
- the simplest set of cells capable of triggering growth of the would-be organ and the initial foundation from which an organ is able to grow.
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primordial cells
cells of the primordium
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Codon usage bias
- differences in the frequency of occurrence of synonymous codons in coding DNA.
- reflect mutation–selection balance for translational optimization.
- optimal codons in fast-growing microorganisms reflect the composition of their respective genomic tRNA pool.
- optimal codons help to achieve faster translation rates and high accuracy.
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mutation–selection balance
a balance between mutational biases and natural selection
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Molecular evolution
the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations
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What does molecular evolution study?
rates and impacts of:
- single nucleotide changes
- neutral evolution vs. natural selection
- origins of new genes
- the genetic nature of complex traits
- the genetic basis of speciation
- evolution of development
- ways that evolutionary forces influence genomic and phenotypic changes.
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Common descent
- when one species is the ancestor of two or more species later in time.
- an effect of speciation, in which multiple species derive from a single ancestral population.
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monophyly (holophyly)
- the condition of being a clade— a group of taxa composed only of an ancestral population and all of its lineal descendants (undergone common descent).
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Monophyletic groups
- typically characterised by synapomorphies, which distinguish organisms in the clade from other organisms.
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synapomorphies
shared derived characteristics
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paraphyly
and polyphyly
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paraphyletic group
all of the descendants of a common ancestor minus one or more monophyletic groups.
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polyphyletic group
- convergent features or habits of scientific interest (for example, night-active primates, fruit trees, aquatic insects).
- features by which a polyphyletic group is differentiated from others are not inherited from a common ancestor.
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branching order
shows group relationships
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branch length
shows about of evolution
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Phylogenetic trees of species and higher taxa are used
to study the evolution of traits (e.g., anatomical or molecular characteristics) and the distribution of organisms (biogeography).
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sister group (sister taxon)
the closest relative(s) of another given unit in an evolutionary tree.
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polymorphism
- the occurrence of two or more clearly different morphs in the population of a species.
- morphs must occupy the same habitat at the same time and belong to a panmictic population
when there are two or more possibilities of a trait on a gene.
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morph
- form
| - alternative phenotype
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How does polymorphism function?
- retain variety of form in a population living in a varied environment
e. g. sexual dimorphism, mimicry and human hemoglobin and blood types.
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Mutation–selection balance
- an equilibrium in the number of deleterious alleles in a population that occurs when the rate at which deleterious alleles are created by mutation equals the rate at which deleterious alleles are eliminated by selection
- does not account for balancing selection or genetic drift
- one of the explanations for how genetic variation is maintained in populations
- also acts to balance selective loss of variation and creation of variation by beneficial mutations
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negative selection (purifying selection)
- selective removal of alleles that are deleterious.
- can result in stabilising selection through the purging of deleterious genetic polymorphisms that arise through random mutations
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background selection
- caused by the strong negative selection on a locus
- the purging of deleterious variants will result in the occasional removal of linked variation, producing a decrease in variation
- the incidental purging of non-deleterious alleles due to such spatial proximity to deleterious alleles
- effect increases with lower mutation rate but decreases with higher recombination rate.
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Purifying selection can be split into
- purging by non-random mating
- purging by genetic drift
- purging by genetic drift can remove primarily deeply recessive alleles, whereas natural selection can remove any type of deleterious alleles.
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Balancing selection
- multiple alleles are actively maintained in the gene pool of a population at frequencies larger than expected from genetic drift alone.
- genetic polymorphism is conserved.
- heterozygote advantage (heterotic balancing selection - balanced polymorphisms.
- frequency-dependent selection.
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heterozygote advantage
when the heterozygotes for the alleles under consideration have a higher fitness than the homozygote.
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overdominance
- another term for heterozygote advantage and the resulting balancing selection
- because heterozygotes are more common than mathematically predicted
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Frequency-dependent selection
occurs when the fitness of a phenotype is dependent on its frequency relative to other phenotypes in a given population.
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In positive frequency-dependent selection
the fitness of a phenotype increases as it becomes more common.
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In negative frequency-dependent selection
the fitness of a phenotype decreases as it becomes more common.
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prey switching
- frequency-dependent predation
- the predator preferentially consumes the most common species of prey
- rare morphs of prey are fitter due to predators concentrating on the more frequent morphs.
- predation drives the demographic frequencies of the common morph of prey down, the once rare morph of prey becomes the more common morph.
- lead to boom and bust cycles of prey morphs.
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How does the Red Queen hypothesis align with negative frequency-dependent selection?
Through host-parasite interactions may also drive negative frequency-dependent selection, in alignment with the Red Queen hypothesis.
- no one phenotypic morph, nor one genotype is entirely extinguished from a population, nor is one phenotypic morph nor genotype selected for fixation; polymorphism is maintained.
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fitness varies in
time and space
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Convergent evolution (in cladistics: homoplasy)
- the process by which related or distantly related organisms evolve independently.
- creates analogous structures
- e.g. repeated development of C4photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals, and carnivory.
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analogous structures
- have a similar function, structure, or form
| - were not present in the last common ancestor of the groups
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Recurrent evolution
- the repeated evolution of a particular trait, character, or mutation.
- when patterns emerge from this stochastic process
- demonstrate the underlying forces governing evolution, and recurring regimes of selection within or across lineages.
- also used to describe recurring patterns of mutation; for example, transitions are more common than transversions.
- encompasses both convergent evolution and parallel evolution
- describes the observation of similar repeating changes through directional selection as well as the observation of highly conserved phenotypes or genotypes across lineages through continuous purifying selection over large periods of evolutionary time.
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Parallel evolution
- the similar development of a trait in distinct species that are not closely related, but share a similar original trait in response to similar evolutionary pressure
- can arise from co-evolution
- e.g. predator-prey, pollinator-plant
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Adaptive evolution
- evolutionary changes that happen due to the changes in the environment, this makes the organism suitable to its habitat.
- E.g. Darwin’s finches
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Divergent evolution (divergent selection)
- the accumulation of differences between closely related populations within a species, leading to speciation.
- typically exhibited when two populations become separated by a geographic barrier and experience different selective pressures that drive adaptations to their new environment.
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adaptive radiation
- organisms diversify rapidly from an ancestral species into a multitude of new forms, particularly when a change in the environment makes new resources available, alters biotic interactions or opens new environmental niches
- starting with a single ancestor, this process results in the speciation and phenotypic adaptation of an array of species exhibiting different morphological and physiological traits.
- e.g. finch speciation on the Galapagos ("Darwin's finches")
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Peripatric speciation
- a mode of speciation in which a new species is formed from an isolated peripheral population
- one of the populations is much smaller than the other.
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centrifugal speciation
a species' population experiences periods of geographic range expansion followed by shrinking periods, leaving behind small isolated populations on the periphery of the main population.
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Character displacement
differences among similar species whose distributions overlap geographically are accentuated in regions where the species co-occur, but are minimized or lost where the species' distributions do not overlap.
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Competitive release
the expansion of an ecological niche in the absence of a competitor
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Reinforcement
- a process of speciation where natural selection increases the reproductive isolation (further divided to pre-zygotic isolation and post-zygotic isolation) between two populations of species.
- result of selection acting against the production of hybrid individuals of low fitness.
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Secondary contact
- the process in which two allopatrically distributed populations of a species are geographically reunited.
- potential for the exchange of genes, dependent on how reproductively isolated the two populations have become.
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Primary outcomes of secondary contact
- extinction of one species
- fusion of the two populations back into one
- reinforcement
- the formation of a hybrid zone
- the formation of a new species through hybrid speciation
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hybrid zone
where the ranges of two interbreeding species or diverged intraspecific lineages meet and cross-fertilize.
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Hybrid speciation
hybridization between two different species leads to a new species, reproductively isolated from the parent species.
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Evo-devo:
- the different processes of development can play a role in how a specific organism reaches its current body plan.
- compares the developmental processes of different organisms to infer the ancestral relationships between them and how developmental processes evolved.
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homeotic genes
genes which regulate the development of anatomical structures
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Mutations in homeotic genes cause
- homeosis, and the development of ectopic structures
| - usually lethal.
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homeosis
- displaced body parts
- the transformation of one organ into another, arising from mutation in or misexpression of certain developmentally critical genes
- helped insects become as successful and diverse as they are
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Ontogeny (ontogenesis)
the origination and development of an organism (both physical and psychological, usually from the time of fertilization of the egg to adult.
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A body plan, Bauplan (German plural Baupläne), or ground plan
- a set of morphological features common to many members of a phylum of animals
- evolutionary developmental biology seeks to explain the origins of diverse body plans.
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example features of a body plan
- symmetry
- layers
- segmentation
- limb
- gut disposition.
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evo-devo gene toolkit
the small subset of genes in an organism's genome whose products control the organism's embryonic development.
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deep homology
where growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species
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Biogeography
the study of the distribution of species and ecosystems in geographic space and through geological time.
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Panmixia
- the mating between two organisms is not influenced by any environmental, hereditary or social interaction.
- potential mates have an equal chance of being selected.
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Evolution in action
- peppered moths
- flightless birds
- lactose tolerance
- sickle-cell anemia persistence
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homology
- similarity due to shared ancestry between a pair of structures or genes in different taxa
- explained by descent with modification from a common ancestor.
- e.g. forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure.
e. g.2. dominance hierarchy in primates
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Antigenic variation (antigenic alteration)
- pathogen alters the proteins or carbohydrates on its surface and thus avoids a host immune response
- one of the mechanisms of antigenic escape.
- allows re-infection of previously infected hosts
- means that even a clonal population of pathogens expresses a heterogeneous phenotype
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How does antigenic variation arise?
- gene conversion
- site-specific DNA inversions
- hypermutation
- recombination of sequence cassettes
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Antigenic escape (immune escape/ immune evasion/ escape mutation)
- when the immune system of a host is unable to respond to an infectious agent; no longer able to recognize and eliminate a pathogen such as a virus.
- inhibiting neutrophils and macrophages
- a pathogen's epitopes become too similar to a person's naturally occurring MHC-1 epitopes; the immune system becomes unable to distinguish the infection from self-cells
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epitope (antigenic determinant)
- the binding sites for immune cells
- the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells
- the specific piece of the antigen to which an antibody binds.
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phase variation is
- a method for dealing with rapidly varying environments without requiring random mutation
- variation of protein expression, frequently in an on-off fashion, within different parts of a bacterial population
- contributes to virulence by generating heterogeneity
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paratope
The part of an antibody that binds to the epitope
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Somatic hypermutation (or SHM)
- a cellular mechanism by which the immune system adapts to the new foreign elements that confront it
- programmed process of mutation affecting the variable regions of immunoglobulin genes.
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Mistargeted somatic hypermutation is a likely mechanism in the development of
B-cell lymphomas and many other cancers.
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sequence alignment
a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences
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conserved sequences
identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences)
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A highly conserved sequence is one that has
remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time.
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Pleiotropy (from Greek πλείων pleion, 'more', and τρόπος tropos, 'way')
- when one gene influences two or more seemingly unrelated phenotypic traits.
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pleiotropic gene
a gene that exhibits multiple phenotypic expression
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Mutation in a pleiotropic gene may
have an effect on several traits simultaneously, due to the gene coding for a product used by a myriad of cells or different targets that have the same signaling function.
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How does pleiotropy arise?
- gene pleiotropy
- developmental pleiotropy
- selectional pleiotropy
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Gene pleiotropy occurs
when a gene product interacts with multiple other proteins or catalyzes multiple reactions.
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Developmental pleiotropy occurs
when mutations have multiple effects on the resulting phenotype.
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Selectional pleiotropy occurs
when the resulting phenotype has many effects on fitness (depending on factors such as age and gender).
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Pleiotropic gene action can
limit the rate of multivariate evolution when natural selection, sexual selection or artificial selection on one trait favors one allele, while selection on other traits favors a different allele.
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Genetic architecture
the underlying genetic basis of a phenotypic trait and its variational properties
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Gene regulation:
- transcriptional initiation
- RNA processing
- post-translational modification of a protein.
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gene regulatory network
often, one gene regulator controls another
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lac operon
some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.
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quantitative trait locus (QTL)
- a locus that correlates with variation of a quantitative trait in the phenotype of a population of organisms.
- mapped by identifying which molecular markers correlate with an observed trait.
- often an early step in identifying and sequencing the actual genes that cause the trait variation.
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QTL traits are affected by
- gene and allele number
- the distribution of allelic and mutational effects
- patterns of pleiotropy, dominance, and epistasis
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Flightless birds
birds that through evolution lost the ability to fly.
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totally flightless birds are a result of
selective breeding; the birds were bred to grow massive breast meat that weighs too much for the bird's wings to support in flight.
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Gigantism and
flightlessness are almost exclusively correlated.
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Flightlessness coincides with
body mass, because energy expenditure required for flight increases proportionally with body size
- by reducing large pectoral muscles that require a significant amount of overall metabolic energy, ratites decrease their basal metabolic rate and conserve energy
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Adaptations of wings
- necessary for balance
- sexual selection
- indicates protective abilities
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Environmental DNA or eDNA is
DNA that is collected from a variety of environmental samples such as soil, seawater, snow or air, rather than directly sampled from an individual organism.
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How does eDNA accumulate
As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources.
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Sources of eDNA:
- feces
- mucus
- gametes
- shed skin
- carcasses
- hair
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How is eDNA analysed for rapid monitoring and measurement of biodiversity?
high-throughput DNA sequencing methods:
- metagenomics
- metabarcoding
- single-species detection
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Why is DNA metabarcoding used?
In order to better differentiate between organisms within a sample
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DNA metabarcoding
the sample is analyzed and uses previously studied DNA libraries, such as BLAST, to determine what organisms are present.
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Why is eDNA monitored?
- monitoring common species,
- genetically detect and identify other extant species that could influence conservation efforts
- biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism.
- understanding of population size, species distribution, and population dynamics for species not well documented.
- more cost-effective.
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The integrity of eDNA samples is dependent upon
its preservation within the environment.
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Metagenomics (environmental genomics/ecogenomics/community genomics)
- the study of genetic material recovered directly from environmental samples
- early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample.
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What did early metagenomic work reveal?
the vast majority of microbial biodiversity had been missed by cultivation-based methods
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Microbial DNA barcoding
- the use of DNA metabarcoding to characterize a mixture of microorganisms.
- uses universal genetic markers to identify DNA of a mixture of organisms.
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Fossils:
Examples include:
- bones
- shells
- exoskeletons
- stone imprints of animals or microbes
- objects preserved in amber
- hair
- petrified wood
- oil
- coal
- DNA remnants
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the fossil record
the totality of fossils
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Comparative anatomy
- the study of similarities and differences in the anatomy of different species.
- provided evidence of common descent, and has assisted in the classification of animals.
