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5.13: Introduction to the Evolution of Populations - Biology


What you’ll learn to do: Discuss the ways populations evolve

All life on Earth is related. This combination of processes has led to the world of life we see today


Introduction

Living things may be single-celled or complex, multicellular organisms. They may be plants, animals, fungi, bacteria, or archaea. This diversity results from evolution. (credit "wolf": modification of work by Gary Kramer credit "coral": modification of work by William Harrigan, NOAA credit "river": modification of work by Vojtěch Dostál credit "fish" modification of work by Christian Mehlführer credit "mushroom": modification of work by Cory Zanker credit "tree": modification of work by Joseph Kranak credit "bee": modification of work by Cory Zanker)

All life on Earth is related. Evolutionary theory states that humans, beetles, plants, and bacteria all share a common ancestor, but that millions of years of evolution have shaped each of these organisms into the forms we see today. Scientists consider evolution a key concept to understanding life. It is one of the most dominant evolutionary forces. Natural selection acts to promote traits and behaviors that increase an organism’s chances of survival and reproduction, while eliminating those traits and behaviors that are detrimental to the organism. However, natural selection can only, as its name implies, select—it cannot create. We can attribute novel traits and behaviors to another evolutionary force—mutation. Mutation and other sources of variation among individuals, as well as the evolutionary forces that act upon them, alter populations and species. This combination of processes has led to the world of life we see today.


5.13: Introduction to the Evolution of Populations - Biology

INTRODUCTION TO EVOLUTIONARY BIOLOGY

These are not meant to be comprehensive notes but just brief ones on basic evolutionary biology at very introductory level. This page is intended to be the basis for the following discussions of more specialised topics.

1. Major events in evolutionary history

2. Basic concepts in evolutionary biology

Natural Selection, Genetic Drift, Mutation

4. Some rules and theories in evolutionary biology

Major events in evolutionary history

Evolution of eukaryotes from a prokaryotic ancestral cell

Evolution of lungs in amphibians and then land animals

Evolution of amnion, allantois and shelled egg (the conquest of dry land by vertebrates)

Evolution of feathers and wings leading to the evolution of flight

Upright walking and tool using

Artistic inclination and thinking

Basic concepts in evolutionary biology

Evolution is the result of the simultaneous occurrence of multiple causes including (stochastic) chance phenomena and the more deterministic selective phenomena. In the production of variation, chance dominates, while selection itself operates largely by necessity. Any property that evolves must be controlled by a gene that can vary. Evolution is more than merely a change in gene frequencies. It also includes the origin of the variation.

Four processes account for most of the changes in allele frequencies in population

Those that increase genetic variation :

1. Mutation - recombination

Those that decrease genetic variation :

3. Natural selection (stabilizing selection)

4. Random genetic drift (3 & 4 are the most important ones)

All but genetic drift are deterministic ones.

There are two evolutionary dimensions: time (adaptedness) and space (speciations and multiplication of lineages).

Evolution is not progress. It is about adaptation to surroundings. This does not necessarily mean improvement over a period of time. Evolution cannot be equated with progress. However, no progress can take place without it.

Probably all traits are a product of genetic and environmental effects. In general, the more genes are involved, the more continuous is the variation. According to the Fundamental Theorem of Natural Selection, the rate of adaptive change is proportional to the amount of genetic variation in the population. The rate of increase in fitness is equal to the genic variance in the population [RA Fisher 1930].

Evolution can occur without morphological change, and morphological change can occur without evolution. Sibling species are genetically distinct but may be very similar morphologically. Gross evolution tends to be irreversible [Dollo's law]. It would be a mistake, however, to consider evolution totally irreversible. Atavism (the reappearance of certain characters typical of remote ancestors) argues against this.

Only heritable changes contribute to evolution (not environmentally induced phenotypical changes). Behaviour evolves through natural selection similar to the evolution of morphological characters.

Darwin's basic principle: Evolution is due to genetic variation and natural selection acting on heritable characters. Charles Darwin recognized natural selection as the mechanism of evolution in 1838, but did not publish the Origin of Species until 1859. Alfred Russel Wallace reached the same conclusion independently in 1858.

Darwin's five major theories

1. The organisms steadily evolve over time (evolution theory)

2. Different kinds of organisms descended from a common ancestor (common descent theory)

3. Species multiply over time (speciation theory)

4. Evolution takes place through the gradual change of populations (gradualism theory)

5. The mechanism of evolution is the competition among vast numbers of unique individuals for limited resources under selective pressures, which leads to differences in survival and reproduction (natural selection theory)

Weaknesses of Darwin’s natural selection theory

1. Blending inheritance was favoured rather than discrete Mendelian genes (which was unknown at the time)

2. No knowledge of Mendel genetics was available

3. Phyletic gradualism was favoured as the type of speciation

4. Fecundity was not emphasized in the description of fitness

5. Sexual selection: Sexually selected characters were seen as ornaments but they may be advertising genuine male qualities (Hamilton & Zuk, 1982)

Evidence used by Darwin for his natural selection theory

1. Biogeography: Distinct features of cosmopolitan species and the presence of endemic species (Darwin's finches: of the 14 finch species of the Galapagos islands, 13 are endemic)

2. Morphology and embryology: Homologous structures among related species similarities in the embryos of related species

3. Paleontology: Gradual change in the fossil record, evident extinctions

4. Taxonomy and systematics: Morphological similarities among related taxa

In evolution, it is not the survival of the individual that matters but of the offspring of that individual (relevant in altruism).

Natural selection is one mechanism responsible for evolutionary change. It does not act on species or on populations, but on [the phenotypes not genotypes of] individuals. Genes mutate, individuals are selected, populations evolve. Natural selection is the non-random survival of randomly varying hereditary characteristics. Evolution acts on the portion of variation, which is controlled genetically. Natural selection favours traits that enhance reproduction.

No gene is ever directly exposed to selection, but only in the context of an entire genotype, and a gene may have different selective values in different genotypes (i.e., the gene is not the target of selection). An individual is favoured by selection owing to the overall quality of its genotype. This is a confusing issue in modern evolutionary biology. This arises from the fact that in classical Darwinian school, it is believed that the unit of selection is the individual but in neo-Darwinism (the New Synthesis), it is the gene. The classical belief that the unit of selection is the individual is true within any one generation, but there is no continuity in individuals in a sexually reproducing species, the only continuity is in the continuation of copies of alleles. This is why the New Synthesis considers selection to act on particular alleles in relation to their average contribution to all the individuals that carry copies of them.

1. Stabilizing: Most adaptive character is preserved as long as the adaptive peak does not change. A typical example of stabilizing selection was presented by H. Bumpus in 1899. He measured the wings of house sparrows (Passer domesticus) killed in a storm in New York. He found that those with markedly long or short wings were more frequently killed. Stabilizing selection does not allow new variations to emerge. Once a character is optimised, natural selection keeps it as it is like keeping the number of fingers, egg size and number, mate choice adaptations, seasonal timing of migrations, birth weight in humans etc. stable. Both extremes in variation are selected against and eliminated. Aristotle's description of wild animals and plants, written 2,500 years ago, are still accurate today as natural selection must have been preventing their further evolution [from a stable state]. Thus, natural selection cannot be equated to evolution as sometimes it prevents evolution, but it is a major mechanism involved in evolution.

2. Directional: Strong selection favours one of the extreme phenotypes. This type of selection decreases variation (sexual selection of male characters). Antibiotic resistance by bacteria and insecticide resistance by insects are other examples. By favouring those who are resistant, the variation in the population decreases, and the population eventually consists of only resistant individuals. A common form of directional selection causes character displacement when two species compete. When there are two species of finches on an island, each will evolve to have a different size beak (small and large) whereas either species alone has an intermediate beak size elsewhere.

3. Disruptive selection (heterozygote disadvantage or homozygote advantage): Both extreme phenotypes are preferred over the intermediate one. This selection occurs as a result of the heterozygotes being at a disadvantage, thus the two homozygotes are selected (underdominance). In a bi-allelic polymorphism, if one of the alleles is remarkably rare than the other, the rare allele may be lost. Selection for two different colours in North American lacewings but not for intermediate colour is an example. This happens because the two extreme colour patterns provide the best camouflage in the two different niches but the intermediate one does not offer any protection. Similarly, the African swallowtail butterfly produces two distinct morphs, both of which mimic distasteful butterflies of other species with aposematic coloration (Batesian mimicry). This type of selection tends to increase or maintain the diversity in the population. It might even cause one species to evolve into two .

Evolution requires genetic variation. Mutation is a change in a gene (variation). Natural selection operates on this variation and the population evolves. Natural selection is the only mechanism and the driving force of adaptive evolution. The most common action of natural selection is to remove unfit variants as they arise via mutation (most mutations are lost due to drift). Selection only distinguishes between existing variants, does not create new ones. Without selection, genetic diversity would be low and primarily controlled by two parameters: how frequently new alleles arise due to mutation (or immigration) and how frequently alleles are lost due to genetic drift, which is dependent on the size of the population.

Constraints on natural selection

1. Natural selection does not induce variability. The genetic variation needed for the most adaptable phenotype may not be available or forthcoming,

2. The different components of the phenotype are dependent of one another and none of them can respond to selection without interacting with the others,

3. Most genes are pleiotropic and most components of the phenotype are polygenic characters,

4. Capacity of organisms for non-genetic modifications: the more plastic the phenotype is (owing to developmental flexibility), the more this reduces the force of adverse selection pressures,

5. Much of the differential survival and reproduction in a population is still the result of chance. This also limits the power of natural selection.

Natural selection is often confused with evolution. The original definition of evolution was descent with modification. This includes both the origin as well as the spread of new variants or traits. Evolution may thus occur as a result of natural selection, genetic drift, or both, as long as there is a continual supply of new variation (such as mutation, recombination, gene flow). Natural selection does not necessarily give rise to evolution. Unlike evolution, natural selection is a non-historical process that depends upon only current ecological and genetic conditions. Evolution depends not only on these current conditions but also upon their entire history. Natural selection deals with frequency changes brought about by differences in ecology among heritable phenotypes evolution includes this as well as random effects and the origin of these variants.

Natural selection does not have any foresight. It only allows organisms to adapt to their current environment. Selection merely favours beneficial genetic changes when they occur by chance. Neither mutations arise as an adaptive response to the environment, but may prove fortuitously to be adaptive after they arise. Unstable environments drive and induce evolution. Environment does not cause change, it causes the need for change, which is recognized and acted upon by the organism. Think about why all trees in a rain forest are tall. What happened to the short ones?

Most major evolutionary changes occur by the gradual accumulation of minor mutations, accompanied by very gradual phenotypic transitions.

Evidence for evolution by natural selection in contemporary populations:

1. The resistance of the house fly (Musca domestica) to DDT first reported in 1947,

2. The change in the frequencies of differently coloured peppered moths with industrial revolution in England,

3. Establishment of new HLA alleles in isolated and inbred populations where most subjects would be homozygous and new alleles increasing heterozygosity rate would be favoured.

Random Genetic Drift : Populations do not exactly reproduce their genetic constitutions in successive generations. There is a random/chance component of gene-frequency change. In other words, only a fraction of all possible zygotes become mature adults and not all alleles available in parental gene pool are transmitted to the offspring. If a pair of parents has one child, not all of their alleles will have passed on to the next generation. In a large population, the random nature of the process will average out. But, in a small population the effect could be rapid and significant. Random genetic drift is a change in the allele frequencies in a population that cannot be ascribed to the action of any selective process. It is a binomial sampling error of the gene pool.

In principle, any individual may by chance meet with an accident or fail to meet a mate, and so fail to make a contribution to the next generation, irrespective of how well it is adapted. Therefore, its genes will not be represented in the next generation. This is not important in a large population. In small populations, such chance happenings can have important effects on gene frequencies and the population may drift away from the adaptive peak. Genetic drift can be an aid as well as a hindrance to adaptation.

Like natural selection, drift also decreases genetic variation. There are, however, mechanisms that replace variation depleted by selection and drift (mutation -the most important one-, recombination, gene flow). Genetic drift and natural selection are the two most important mechanisms of evolution. Their relative importance depends on estimated population sizes. Drift is much more important in small populations and in those who breeds in demes. In principle, genetic drift acts on a smaller time scale and natural selection in the long-term.

See simulations of genetic drift concept: simulation-1 & simulation-2 .

Genetic bottleneck : Sudden and remarkable reduction in the population size due to natural disasters, disease, or predation ( North ern elephant seal population at the end of the last century American buffalo population in the beginning of this century, and cheetahs). The small number of survivors may represent only a fraction of the original polymorphism present in the population. When the population grows to large numbers, genetic variation may be limited. The cheetah appears to have gone through a population bottleneck, probably at the end of the Pleistocene. Because of the limited variation in the population, in the mid-1980s, an outbreak of feline infectious peritonitis caused 50-60% mortality rate showing the importance of genetic diversity in maintaining healthy populations.

Genetic drift caused by bottlenecking may have been important in the early evolution of human populations when calamities decimated tribes. The unselected small group of (lucky) survivors is unlikely to be representative of the original population in its genetic make-up (this is an example of evolution by luck but not by fitness).

When a population has been founded by a few or even by a single gravid female, this population cannot contain more than a fraction of the total genetic variability of the parent population. This is called founder effect. When a population is started by one or a small group of individuals randomly separated from the parent population, chance may dictate that the allele frequencies in the newly founded population will be quite different from those of the parent population. Many species on islands (Drosophila of Hawaii, Darwin's finches at Galapagos) display the consequences of founder effects.

In any population, some proportion of loci is fixed at a selectively unfavourable allele because the intensity of selection is insufficient to overcome the random drift to fixation. Drift is intensified as selection pressures increase. This is because, strong selection decreases the effective population size.

If the genetic variation observed in populations is inconsequential to survival and reproduction (ie, neutral), the drift will be the main determinant. If the gene substitutions affect fitness, natural selection is the main driving force.

Mutation provides the new and different genetic raw material for evolution. It is the ultimate source of all new genetic variation. Mutations are frequently reversible, being able to mutate back to normal. Some genes are prone to recurring, often similar, mutations. Advantageous gene mutations are retained in a population, while deleterious ones tend to be eliminated because its inheritors are not as viable.

The rate of mutation per base per replication is approximately 10 -9 (10 -5 to 10 -6 per gene per generation). Chromosomal mutations are more common. For example, reciprocal translocations occur at a rate of 10 -4 to 10 -3 per gamete per generation. Most mutations are thought to be neutral with regards to fitness. A change in environment can cause a neutral allele to have a selective value. In the short term, evolution can run on stored variation for which mutation is the ultimate source.

Pseudogenes evolve much faster than their working counterparts (the same applies to introns). Mutations in them do not get incorporated into proteins, so they are not subject to selection. Also, silent nucleotide sites (that can be changed without changing the sequence of the protein) are expected to be more polymorphic than replacement nucleotide sites within a population and show more differences between populations. This is because silent changes are not subject to selection.

As the neutral theory predicts, the rate of evolution is greater in functionally less constrained molecules. Proteins with vital functions cannot tolerate mutations as they would interfere with the viability of the organism.

Li and Graur (1991) calculated the rate of evolution for silent vs. replacement sites in humans and rodents. Silent sites evolved at an average rate of 4.61 nucleotide substitution per 10 9 years. Replacement sites evolved much slower at an average rate of 0.85 nucleotide substitution per 10 9 years.

Most neutral alleles are lost soon after they appear. Alleles are added to the gene pool by mutation at the same rate they are lost to drift. For neutral alleles that do fix, it takes an average of 4Ne generations (Ne = effective population size) to do so. When a new allele has a positive selective value, s, the expected time to fixation is less than 4Ne generations and is, approximately, (2/s)loge(2Ne) generations (Ayala FJ, 1994).

Deleterious mutants are selected against but remain at low frequency in the gene pool. In diploids, a deleterious recessive mutant may increase in frequency due to drift (unopposed by selective forces). Deleterious alleles also remain in populations at a low frequency due to a balance between recurrent mutations and selection (the mutation load). It is estimated that each of us, on average, carries three to five recessive lethal alleles.

Most new mutants, even beneficial ones, are lost due to drift (but may recur many times). An allele that conferred a one percent increase in fitness has only a two percent chance of fixing. A beneficial mutant may be lost several times, but eventually it will arise and stick in a population. Even deleterious mutations may recur. Directional selection depletes genetic variation at the selected locus as the fitter allele sweeps to fixation. Sequences linked to a selected allele also increase in frequency due to hitchhiking. Eventually, recombination will bring the two loci to linkage equilibrium (their association will be random).

Recombination within a gene can form a new allele. Recombination is a mechanism of evolution because it adds new alleles and combinations of alleles to the gene pool.

Genetic drift, gene flow and the breeding structure of a species should, in principle, affect all loci in a similar fashion.

Neutralism : According to the neutral theory of molecular evolution, the great majority of evolutionary changes at the molecular level do not result from natural selection but, rather, from random fixation of selectively neutral or near-neutral mutants through random genetic drift. It assumes that only a minute fraction of molecular changes are adaptive and most mutations are selectively neutral (neither advantageous nor non-advantageous). As a result, polymorphisms are maintained by the balance between mutational input and random extinction. The frequency of synonymous base changes in a population is a matter of genetic drift not natural selection. Molecular changes that are less likely to be subject to natural selection occur more rapidly in evolution. Thus, neutral evolution occurs at higher rate. Initially, a wide variety of observations seemed to be consistent with the neutral theory. Eventually, however, several lines of evidence have emerged arguing against it.

Inbreeding leads to an increase in homozygosity at all loci because the breeding pairs are initially genetically more similar to one other than would be the case if a pair of individuals had been taken at random from the population. Inbreeding distributes genes from the heterozygous to homozygous state without changing the allele frequencies. Outbreeding does not eliminate but preserves deleterious alleles in heterozygous state (masking effect). Self-fertilization, the most extreme case of inbreeding, most definitely eliminates them.

Balancing selection involves opposing selection forces. A balanced equilibrium results when two alleles selected against in the homozygous state are retained because of the superiority of heterozygotes (heterozygote advantage or overdominance). This is why a recessive deleterious allele will never be eliminated by selection as it will be maintained in heterozygous form. Selection can maintain a polymorphism when the heterozygote is fitter than either homozygote.

In many mammals, including humans, more than 50% of zygotes are male and, for reasons that are poorly understood, this proportion gradually falls between conception and birth. The primary sex ratio is estimated to be at least 120 (males):100 (females) at conception in humans [McMillen et al, Science 1979204:89]. This is evidence for prenatal selection and it appears that an MHC-mediated, male-specific selection based on heterozygous advantage is operating [Dorak et al, Genes & Immunity 20023:263-9].

The alleles that increase in frequency relative to others are said to be fitter, so the change in these relative frequencies measures neo-Darwinian fitness. Fit does not necessarily mean biggest, fastest or strongest. Evolutionary fitness refers to reproductive success and survival.

Mendel's ideas : Heterozygous parents produce equal quantities of gametes containing the contrasting alleles genes of different characters behave independently as they are assorted into gametes genes are non-blending and very stable (he did not use the word gene but meant it). Identical looking individuals may be genetically different since part of the genetic variety is masked by dominance.

Mendel's first law (law of segregation): The two alleles received one from each parent are segregated in gamete formation, so that each gamete receives one or the other with equal probability.

Mendel's second law (law of recombination): Two characters determined by two unlinked genes are recombined at random in gametic formation, so that they segregate independently of each other, each according to the first law. (Note that recombination here is not used to mean crossing-over in meiosis.)

In diploid organisms, the extent to which an allele spreads or recedes in a population depends upon which alleles it becomes associated with in heterozygotes. For example, a recessive deleterious gene will be protected from selection in heterozygous associations with advantageous dominants. Alternatively, selection against a deleterious dominant will lead to the elimination of advantageous recessives when they are associated with it in the heterozygotes.

Similarities of the proteins of coding region DNAs of two species may be due to convergent evolution or similarity by descent. But, similarities in non-coding region DNAs can only be similarity by descent and it means that these two species have only recently diverged.

The largest amount of human genetic diversity is being preserved in African genomes. Evolutionarily speaking, Africans thus have a larger allelic pool to draw on for both fitness and survival. [See Disotell TR: Sex-specific contributions to genome variation. Curr Biol 19999:R29 and Olerup et al. HLA-DR and -DQ gene polymorphism in West Africans is twice as extensive as in North European Caucasians, PNAS 199188:8480.]

1. The production of gametes by meiosis

2. The recombination of genes by crossing-over

3. The random allocation of homologous chromosomes to each meiotic product

4. The production of new individuals by syngamy (fusion of two gametes usually from two separate individuals except in self-fertilization). Sexual reproduction generates diversity within populations (evolutionary plasticity) whereas parthenogenesis limits diversity.

Sexual reproduction exposes a new array of genotypes to the environment at each generation, while keeping its basic elements, the alleles, and their respective frequencies about the same. As a result, populations of sexually reproducing organisms enjoy adaptability in the face of a changing environment far beyond the reach of the asexual species. Sexual reproduction may have evolved because of the benefit of having two copies of a gene. This is more adaptive in terms of DNA repair and elimination of a deleterious mutation.

Death : Natural selection cannot prevent senescence and death because it cannot eliminate certain kinds of alleles. The alleles that exert their deleterious effects after an organism has ceased reproducing cannot be eliminated from the gene pool (like Huntington’s chorea, Alzheimer’s disease, late-onset malignancies). Death is an effect of natural selection but is not a character favoured by it. Most popular theories of senescence are antagonistic pleiotropy and mutation accumulation theories.

Extinction : Extinction is the ultimate fate of all species. More than 99.9% of all evolutionary lines that once existed on earth have become extinct. The average life span of a species in the paleontological record is 4 million years (Raup DM 1994). The Permian extinction (250 mya) was the largest extinction in history. It is estimated that 96% of all species (50% of all families) met their end. Often, the appearance of a new species is instrumental in the extinction of another species. All other things being equal, the risk of extinction is higher for small -peripheral- populations, populations of species of short-lived individuals than for populations of species of long-lived individuals for species with a low intrinsic rate of increase, and for those populations whose environment varies greatly. Very little is known about the actual causes of extinction or about how species extinction relates to population extinction. Most extinction is probably due to several factors acting together, not just a single cause. Species do not become extinct because they fail to adapt. Extinction occurs when their habitat is removed or changed to a state where there will not be enough individuals with an adapted genotype to maintain the species. Extinction via predation by humans is an example. Surely, there was no animal with a genotype adapted to protection from predation by firearms and not enough time was given to them to adapt. Currently, human alteration of the ecosphere is causing a global mass extinction. Extinction is a normal part of evolution, and overall, it has taken place almost as often as speciation.

Some laws and principles in evolutionary biology

Allen's Rule: Within species of warm-blooded animals (birds + mammals) those populations living in colder environments will tend to have shorter appendages than populations in warmer areas.

Allometry Equation : Most lines of relative growth conform to y=bx a where y and x are the two variates being compared, b and a are constants. The value of a, the allometric exponent, is 1 one the growth is isometric allometry is said to be positive when a>1 and negative when a<1.

Biejernik's Principle (of microbial ecology): Everything is everywhere the environment selects.

Bergmann's Rule : North ern races of mammals and birds tend to be larger than Southern races of the same species.

Coefficient of Relatedness : r=n(0.5) L where n is the alternative routes between the related individuals along which a particular allele can be inherited L is the number of meiosis or generation links.

Cope's 'law of the unspecialised ': The evolutionary novelties associated with new major taxa are more likely to originate from a generalized member of an ancestral taxon rather than a specialized member.

Cope’s Rule : Animals tend to get larger during the course of their phyletic evolution.

There is a gradient of increasing species diversity from high latitudes to the tropics (see New Scientist, 4 April 1998, p.32).

Two or more similar species will not be found inhabiting the same locality unless they differ in their ecological requirements, for example in their food or their breeding habits, in their predators or their diseases.

Fisher’s Fundamental Theorem : The rate of increase in fitness is equal to the additive genetic variance in fitness. This means that if there is a lot of variation in the population the value of S will be large. See Frank & Slatkin, 1992 .

Fisher's Theorem of the Sex Ratio : In a population where individuals mate at random, the rarity of either sex will automatically set up selection pressure favouring production of the rarer sex. Once the rare sex is favoured, the sex ratio gradually moves back toward equality.

Galton's Regression Law : Individuals differing from the average character of the population produce offspring which, on the average, differ to a lesser degree but in the same direction from the average as their parents.

Gause's Rule (competitive exclusion principle): Two species cannot live the same way in the same place at the same time (ecologically identical species cannot coexist in the same habitat). This is only possible through evolution of niche differentiation (difference in beak size, root depths, etc.).

Haeckel’s Law (the infamous biogenetic law): Ontogeny recapitulates phylogeny, i.e., an embryo repeats in its development the evolutionary history of its species as it passes through stages in which it resembles its remote ancestors. (Embryos, however, do not pas through the adult stages of their ancestors ontogeny does not recapitulate phylogeny. Rather, ontogeny repeats some ontogeny - some embryonic features of ancestors are present in embryonic development (L. Wolpert: The Triumph of Embryo. Oxford University Press, 1991)).

Hamilton's Altruism Theory : If selection favoured the evolution of altruistic acts between parents and offspring, then similar behaviour might occur between other close relatives possessing the same altruistic genes which were identical by descent. In other words, individual may behave altruistically not only to their own immediate offspring but to others such as siblings, grandchildren and cousins (as happens in the bee society).

Hamilton’s Rule (theory of kin selection): In an altruistic act, if the donor sustains cost C, and the receiver gains a benefit B as a result of the altruism, then an allele that promotes an altruistic act in the donor will spread in the population if B/C >1/r or rB-C>0 (where r is the relatedness coefficient).

Hardy-Weinberg Law : In an infinitely large population, gene and genotype frequencies remain stable as long as there is no selection, mutation, or migration.

When there is no selection, mutation, migration (gene flow) in a pan-mictic population in infinite size, the genotype frequencies will remain constant in this population. For a bi-allelic locus where the gene frequencies are p and q:

Selection Coefficient (s): s = 1 - W where W is relative fitness. This coefficient represents the relative penalty incurred by selection to those genotypes that are less fit than others. When the genotype is the one most strongly favoured by selection its s value is 0.

Heritability : the proportion of the total phenotypic variance that is attributable to genetic causes:

h 2 = genetic variance / total phenotypic variance

Natural selection tends to reduce heritability because strong (directional or stabilizing) selection leads to reduced variation.

Lyon hypothesis : The proposition by Mary F Lyon that random inactivation of one X chromosome in the somatic cells of mammalian females is responsible for dosage compensation and mosaicism.

Muller’s Ratchet : The continual decrease in fitness due to accumulation of (usually deleterious) mutations without compensating mutations and recombination in an asexual lineage (HJ Muller, 1964). Recombination (sexual reproduction) is much more common than mutation, so it can take care of mutations as they arise. This is one of the reasons why sex is believed to have evolved.

Protein clock hypothesis : The idea that amino acid replacements occur at a constant rate in a given protein family (ribosomal proteins, cytochromes, etc) and the degree of divergence between two species can be used to estimate the time elapsed since their divergence.

Selection Differential (S) and Response to Selection (R): Following a change in the environment, in the parental (first) generation, the mean value for the character among those individuals that survive to reproduce differs from the mean value for the whole population by a value of (S). In the second, offspring generation, the mean value for the character differs from that in the parental population by a value of R which is smaller than S. Thus, strong selection of this kind (directional) leads to reduced variability in the population.

van Baer’s Rule : The general features of a large group of animals appear earlier in the embryo than the special features .

Further reading

What Evolution Is by Ernst Mayr (Basic Books, 2001)

Biology, Evolution, and Human Nature by TH Goldsmith & WF Zimmerman (John Wiley & Sons, 2000)

The Book of Life by SJ Gould (Norton, 2001)

The Way of the Cell by FM Harold (OUP, 2001)

Evolution by Mark Ridley (Blackwell, 2003)

Evolution by DJ Futuyma (Sinauer, 2005)

Internet Links

Evolution in Action:

Science Magazine - Breakthrough of the Year 2005: Evolution in Action (PDF)


Introduction to Human Evolution

As contemporary humans, we are a product of our evolutionary past. That past can be directly observed through the study of the human fossil record, the materials preserved for archaeological study, and the DNA of living and extinct human populations. This course will provide an overview of human evolutionary history from the present--contemporary human variation in a comparative context--through our last common ancestor with the living great apes, some 5-7 million years in the past. Emphasis will be placed on major evolutionary changes in the development of humans and the methodological approaches used by paleoanthropologists and related investigators to develop that knowledge.

The course will begin by asking basic questions about how evolution operates to shape biological variation and what patterns of variation look like in living humans and apes. We will then look at how the human lineage first began to differentiate from apes, the rise and fall of the Australopithecines, the origin and dispersal of the genus Homo, and eventually the radical evolutionary changes associated with the development of agricultural practices in the past 15,000 years. Throughout the course students will be exposed to the primary data, places and theories that shape our understanding of human evolution.


When Charles Darwin first published his ideas of evolution and natural selection, the field of Genetics had yet to be discovered. Since tracing alleles and genetics is a very important part of population biology and population genetics, Darwin did not fully cover those ideas in his books. Now, with more technology and knowledge under our belts, we can incorporate more population biology and population genetics into the Theory of Evolution.

One way this is done is through the coalescence of alleles. Population biologists look at the gene pool and all available alleles within the population. They then try to trace the origin of these alleles back through time to see where they started. The alleles can be traced back through various lineages on a phylogenetic tree to see where they coalesce or come back together (an alternate way of looking at it is when the alleles branched off from one another). Traits always coalesce at a point called the most recent common ancestor. After the most recent common ancestor, the alleles separated and evolved into new traits and most likely the populations gave rise to new species.

The Coalescent Theory, much like Hardy-Weinberg Equilibrium, has a few assumptions that eliminate changes in alleles through chance events. The Coalescent Theory assumes there is no random genetic flow or genetic drift of alleles into or out of the populations, natural selection is not working on the selected population over the given time period, and there is no recombination of alleles to form new or more complex alleles. If this holds true, then the most recent common ancestor can be found for two different lineages of similar species. If any of the above are in play, then there are several obstacles that have to be overcome before the most recent common ancestor can be pinpointed for those species.

As technology and understanding of the Coalescent Theory become more readily available, the mathematical model that accompanies it has been tweaked. These changes to the mathematical model allow some of the previously inhibitive and complex issues with population biology and population genetics have been taken care of and all types of populations may then be used and examined using the theory.


On the origin and evolution of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.


Many emerging invasive species display evidence of rapid adaptation. Contemporary genetic studies demonstrate that adaptation to novel environments can occur within 20 generations or less, indicating that evolutionary processes can influence invasiveness. However, the source of genetic or epigenetic variation underlying these changes remains uncharacterised. Here, we review the potential for rapid adaptation from standing genetic variation and from new mutations, and examine four types of evolutionary change that might promote or constrain rapid adaptation during the invasion process. Understanding the source of variation that contributes to adaptive evolution in invasive plants is important for predicting future invasion scenarios, identifying candidate genes involved in invasiveness, and, more generally, for understanding how populations can evolve rapidly in response to novel and changing environments.

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Introduction

Living things may be single-celled or complex, multicellular organisms. They may be plants, animals, fungi, bacteria, or archaea. This diversity results from evolution. (credit "wolf": modification of work by Gary Kramer credit "coral": modification of work by William Harrigan, NOAA credit "river": modification of work by Vojtěch Dostál credit "fish" modification of work by Christian Mehlführer credit "mushroom": modification of work by Cory Zanker credit "tree": modification of work by Joseph Kranak credit "bee": modification of work by Cory Zanker)

All life on Earth is related. Evolutionary theory states that humans, beetles, plants, and bacteria all share a common ancestor, but that millions of years of evolution have shaped each of these organisms into the forms we see today. Scientists consider evolution a key concept to understanding life. It is one of the most dominant evolutionary forces. Natural selection acts to promote traits and behaviors that increase an organism’s chances of survival and reproduction, while eliminating those traits and behaviors that are detrimental to the organism. However, natural selection can only, as its name implies, select—it cannot create. We can attribute novel traits and behaviors to another evolutionary force—mutation. Mutation and other sources of variation among individuals, as well as the evolutionary forces that act upon them, alter populations and species. This combination of processes has led to the world of life we see today.


Discussion

Species introductions can precipitate rapid evolutionary responses in native species [12,41,42]. Several criteria have been proposed to identify cases of rapid adaptive evolution [5]. Among the most important criteria are directional selection with a known cause, an additive genetic basis for traits under selection, and that the response to selection is likely adaptive. We believe our study adequately addresses all of these elements. First, size-selective predation by fish imposes strong directional selection on populations of Daphnia [16,22,23,43], and in Sierra Nevada lakes the most conspicuous change in the selective environment is the recent introduction of salmonid fishes. Second, because we utilized a common garden experimental design, observed differences among our populations are genetic in nature. Furthermore, traits under selection in this study are known to show significant heritabilities in other species of Daphnia [44,45] and often have substantial levels of additive genetic variation [28]. Finally, the phenotypic response to directional selection is likely to be adaptive because changes we observed are consistent with expectations for populations under size-selective predation. Also useful in identifying rapid evolution is knowledge of the time scale in which the change has taken place and measures of character states before and after the selection event. Because the history of fish introductions is well documented in the Sierra Nevada we know the date of the initial fish stocking in our experimental lakes and the duration of exposure to altered predation regimes. Since this study is cross-sectional and not a temporal series we do not know with certainty what the Daphnia phenotypic states in the fish lakes were prior to fish introductions and subsequent selection. However, given that the three fishless lakes we examined did not differ from one another phenotypically, our assumption that phenotypic trait values from populations that have never been exposed to introduced salmonids are representative of trait values in populations prior to fish introductions is justified.

Our results show that introductions of novel fish predators are associated with a specific pattern of phenotypic change in Daphnia populations from alpine lakes in the Sierra Nevada. In comparison to historically fishless lakes, D. melanica that co-occur with introduced fish are smaller, have smaller offspring, reach maturity earlier and have shorter adult instar durations. Our results are in agreement with other studies showing that the introduction of non-native fish into fishless habitats produces a predictable pattern of rapid divergence from populations not containing fish (e.g., [13]).

The reduced body size observed in D. melanica populations that co-occur with introduced salmonids is consistent with other empirical observations of zooplankton responses to size-selective vertebrate predation. At the community level, size-selective predation by fish results in a shift in species composition such that smaller bodied species become numerically abundant. This shift in species composition can lead to a decrease in maximum zooplankton body length in as little as 20 years [22]. Furthermore, examination of trout stomach contents show they not only contain a higher proportion of larger-bodied zooplankton species within a lake, but that trout preferentially feed upon genotypes conferring relatively larger body sizes within populations of vulnerable species[23]. The effect of size selective fish predation within a population can manifest over quite short periods of time. For example, mean body size decreased when Daphnia were exposed to fish predation for only 50 days [44].

In addition to changes in body size, introductions of fish into naive Daphnia populations of the Sierra Nevada also resulted in changes in life-history strategies. Populations exposed to fish predation mature earlier and had fewer, smaller offspring in each clutch than populations from fishless lakes. The changes in clutch size and timing of reproduction are not surprising since these traits frequently co-vary with body size in Daphnia [46]. Smaller Daphnia tend to carry fewer and/or smaller offspring [47-49].

While we observed a significant correlation between trait divergence and the duration of exposure to fish (Fig. ​ (Fig.3) 3 ) there was considerable variation among lakes in the degree of apparent evolutionary response. The variation in divergence among populations may be due to differences in the initial levels of additive genetic variation or in differences in the intensity of selection. The intensity of selection can greatly affect the rate at which adaptive changes occur. In these alpine lakes differences in the intensity of selection could be the result of varying levels of spatial heterogeneity and fish density among lakes. The relationship between fish density and the intensity of selection has been demonstrated by Cousyn et al. [16] who utilized comparisons across a temporal series of Daphnia resting eggs collected from lake bottom sediments to show that average body size of Daphnia decreased when fish were most dense and increased when fish were least dense.

Map of collection sites in the Sierra Nevada of California, USA. Sites with no history of salmonid introductions are denoted by (△) and sites with a known history of introductions and resident fish populations by (○).

Our estimates of divergence rates for body size and timing of reproduction are several times to an order of magnitude lower than those obtained in a comparable study of the evolutionary response of Trinidad guppies to introduced fish predators [13]. One explanation for the lower observed rates is that much of the evolution in these populations occurred shortly after fish introductions, resulting in overestimates of the actual time during which evolution actually took place. The possibility of protracted sampling would then result in underestimates of the actual rate of phenotypic change. A second possibility for this observation is that the strength of selection in the Sierra Nevada Daphnia populations is not as intense as in the Trinidad guppy system. There are also a number of features of the biology of Daphnia that may contribute to a slower response to selection. Since Daphnia in these populations hatch from an "egg bank" [50] of diapausing eggs in lake bottom sediments there is a continual input of genotypes from earlier time periods. Genotypes from these earlier time periods may have never been exposed to the novel selective regime or had genotypic values that had not advanced as far in response to selection. The effect of this temporal mixing of genotypes would be to retard the realized rate of evolution [51]. In addition, our estimates of the rate of adaptation is based on the simplifying assumption that one calendar year is equal to one generation. For temporary pond populations of Daphnia this is a reasonable assumption since these populations typically engage in a bout of sexual reproduction every year. However, for permanent lake-dwelling populations of Daphnia the reproductive cycle can be more complicated. Lake-dwelling populations may engage in sexual reproduction at highly irregular intervals with clones persisting for long periods of time via asexual reproduction. If the Sierra Nevada populations have engaged in sexual reproduction less frequently than on a yearly cycle our estimated rates would be lower than the actual per generation rates. Alternation of asexual and sexual reproduction may also influence the response to selection in two additional ways. First, a cyclic parthenogenetic mode of reproduction can induce oscillations of expressed genetic variation with low levels of expressed variation during periods of prolonged asexual reproduction punctuated by periods of enhanced expressed genetic variation immediately following a bout of sex [52]. During periods of reduced expressed genetic variation populations would respond to phenotypic selection slowly. Second, the response to selection during periods of asexual reproduction can induce substantial gametic phase disequilibria (GPD non-independence of allele identities at two or more loci). Sexual reproduction and recombination erodes GPD and, assuming an additive genetic basis to the trait, causes a shift in the mean phenotype in the opposite direction from that promoted by selection. This phenomenon is often referred to as genetic slippage and has been observed in a number of populations of Daphnia [28,53,54].


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