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http://biolmolgen.slam.katowice.pl. Evolutionary Genetics. Genetics I Aleksander, L. Sieroń Dept. Molec. General Biol. & Genet. Katowice 2011/12. All the evolutionary process is interpreted today in terms of populations, not individuals. Evolution of Life

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Evolutionary genetics

http://biolmolgen.slam.katowice.pl

Evolutionary

Genetics

Genetics I

Aleksander, L. Sieroń

Dept. Molec. General Biol. & Genet.

Katowice 2011/12


Evolutionary genetics

  • All the evolutionary process is interpreted today in terms of populations, not individuals.

  • Evolution of Life

  • Look around you, and you'll have a sense of enormous diversity in life on Earth. But if you take a closer look, you'll find the similarities are much more important than you would think:

  • every living creature uses the same principal atoms (C, H, N, O, P, S);

  • those atoms make up the same biomolecules (amino acids, fats, sugars and nucleic acids);

  • every living creature uses the same „three-character alphabet" of 4 bases for their genetic information;

  • the same energy molecule is utilized (ATP);

  • the chemical pathways are common;

  • the structure of the cell is very similar in all living organisms.


Evolutionary genetics

Evolution of Life

The facts point to a common origin of all the living organisms on Earth.

All this only became apparent by the XIX century, when the evolution theories surfaced for the first time with enough strength to be accepted.

The first blow on the Fixism, that was accepted until that time, was delivered by Lyell in 1830. Lyell proposed a theory, latter called Principle of the actual causes, that states that the same geological forces that act on Earth now, were acting ages ago. This theory makes enough "room" in the age of Earth for a slow modification of the species.

The center of discussion shifts from the existence or not of evolution, to the way evolution is acting.


Evolutionary genetics

Evolution of Life

Lamarck's Theory of evolution

The first serious attempt of an explanation for the mechanism of evolution was made by Lamarck, the author of the word Biology. Lamarck was a well known botanist, but was set aside by his fellow scientists after his theory of evolution.

Lamarck's theory of evolution was as follows:

changes in environment make the organism "fell the need" to adjust (search for perfection);

the use of an organ makes it bigger, while the opposite reduces it (law of useand disuse);

changes in body structure, acquired during the life of the organism, will be passed on to its descendants (law of transmission of acquired characters).

This theory assumes that the changes are caused by the environment acting upon the organisms and that those changes take place in a short period of time.

This theory was dismissed because the characters acquired would not be passed on to the next generations, because they're only somatic.


Evolutionary genetics

Evolution of Life

Darwin's Theory of evolution

Darwin started to think about the matters of evolution watching the changes he could introduce in the various types of pigeons he bred, and because of the works of Malthus about human population growth.

Malthus proposed that the human population grows much faster than the food it needs, so vast numbers would starve very soon, unless the "less fit" were cut down. In Malthus book, the "less fit" were the poor uneducated english people and all foreigners. This racist way of thinking did not strike Darwin, but made him think of how animal populations behave in nature.

Darwin noticed that, in natural populations, that problem never exists, populations are in an equilibrium with the resources, unless some dramatic changes occur.

Darwin proposed that the population stays at that equilibrium point because the excess organisms are removed by a struggle for life, in the form of a natural selection, that kills the not so well adapted to the environmental conditions of the moment.


Evolutionary genetics

  • Evolution of Life

  • Darwin's Theory of evolution

  • Darwin's theory of evolution, or of natural selection is as follows:

  • if the environment allows it, every population will tend to produce an excess of descendants;

  • that excess will give rise to a struggle for life;

  • there is always variation inside a population, not all individuals have the same characteristics;

  • organisms with a competitive advantage at the time, will reproduce more and leave more descendants;

  • over a large period of time, the characteristics of the population will change, adapting them to a new equilibrium.


Evolutionary genetics

  • Evolution of Life

  • Darwin's Theory of evolution

  • In this theory, you have to remember that the concept of most fit is relative and temporal, that is, a character that is favorable now, can mean very little in the whole "pack" of characteristics of the organism or can be bad in a few years, with environmental changes.

  • There are two kinds of selection:

  • artificial selection - Man takes the place of nature in "choosing" the most fit;

  • natural selection - a group of environment forces acting on populations, either in a positive (allowing an organism to survive and reproduce, if it has a well adapted trait) or negative way (killing an organism that has a deleterious trait).


Evolutionary genetics

  • Evolution of Life

  • Darwin's Theory of evolution

  • There are three kinds of natural selection: 

    • stabilizer selection - keeps the more common traits in the population, so it stays about the same over the generations. Acts in a very stable environment;

    • directional selection - "chooses" a specific trait as the best for that particular environment, causing that trait to become more common and well developed in the population. This is the most common type of selection, changing a population's gene pool over a long period of time and in a general "direction" (do not get it confused with some kind of purpose in that action);

    • evolutive  or disruptive selection - keeps the most extreme traits in the population, changing its characteristics over the time. Usually acts after a dramatic change in the environment or in very heterogenic areas. This kind of selection can either form a population with two (or more) very different characteristics or give rise to two different species.


Evolutionary genetics

Evolution of Life

Neodarwinism

The "weak point" in Darwin's theory of natural selection was the origin of that variation inside the populations, the base for natural selection to act upon.


Evolutionary genetics

  • Evolution of Life

  • Neodarwinism

  • What are the main causes of that variation?

  • meiosis - the phenomenon by which gametes, or sex cells, are formed has several ways of increasing variation:

    • separation of homologous chromosomes - the cells resulting from meiosis have only half of the chromosomes of the "mother-cell" and those are chosen by chance, either coming from the father or the mother of the organism;

    • crossing-over - during the separation of the homologous, chromosomes lay side by side, sometimes overlapping each other. During that cross-over process, pieces can become separated from one chromosome and end up pieced together with the other one, mixing up genes with different parental origins.


Evolutionary genetics

  • Evolution of Life

  • Neodarwinism

  • fertilization - the fusion of a particular pair of male and female gametes, after many millions formed;

  • migration - organisms move from one location to another;

  • mutations - mutations alter the hereditary information that is passed on from generation to generation. Mutations can be:

    • genic - change of a few pairs of nucleic acid bases, altering one or a couple genes;

    • chromosomic - changes in chromosome structure or number, usually so damaging that the whole being is unable to live or is seriously handicapped. 


Evolutionary genetics

  • Evolution factors

  • MUTATION

  • This is the only real cause of creation of variability in populations. The effect of this factor on evolution depends on the adaptability it can cause to its bearer. The fact that some alleles are dominant and others are recessive also changes the pattern of "life" of a mutation in a population. There are three kinds of mutations:

    • genic mutations - change only a few base pairs in the chain of DNA;

    • structural mutations - change the number or order by which genes are arranged in the chromosome;

    • numeric mutations - change in the number (2n) of chromosomes. Monossomic (2n-1) and nulissomic (2n-2) mutations are usually deadly, while polissomic (2n+1) mutations cause serious physical and mental problems;


Evolutionary genetics

Evolution factors

NATURAL SELECTION

Can be described as a different chance of living and breeding for any organism.

Organisms having traits that will give them a better chance of breeding and leaving more descendants, will be "chosen" to live.


Evolutionary genetics

Evolution factors

GENETIC DRIFT

Random changes in the population gene pool can happen when the population is very small (under 100 organisms) or when only a few are actually breeding.

These small groups don't have a complete sample of the genetic pool of the population, so that can result in the fixation of some alleles (even if they're not "the best ones" for that particular environment) and the complete loss of others that could've been useful.

This results in a reduction of variability, causing the population to fail to respond to environmental changes, or even becoming extinct;


Evolutionary genetics

Evolution factors

MIGRATION

Most populations live fairly isolated from each other, but there can be migrations, in which the survivers will add new genes to the genetic pool of the receptors (if their genetic background is different to start with, of course).

If the migration rate is low it will act almost as a mutation but if its high enough can become one of the main evolution factors, right up there with natural selection.


Evolutionary genetics

The Origin and Evolution of Life:A Product of Cosmic, Planetary, and Biological Processes

The host of natural phenomena which collectively have created life as we know it.

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

Life apparently requires a solar system having a planet with "suitable" conditions such as liquid water, nutrients, and sources of energy.

Interactions between various substances and energy yielded the autocatalytic systems capable of passing information from one generation to the next, and the thread of life began.

This thread, which has been maintained by DNA molecules for much of its history, is shown weaving its way through the primitive oceans, gaining strength, and gradually acquiring the lineages of organisms whose descendants populate our modern biosphere.

Plants and animals then moved onto the land, where more advanced forms, including humanity, ultimately arose.

Finally, assisted with a technology of its own making, life has reached back out into space to understand its own origins, to expand into new realms, and to seek other living threads in the cosmos.


Evolutionary genetics

Evolution of the Cosmos

Astronomers now believe that the universe began at least 15 billion years ago, when the first clouds of the elements hydrogen and helium were formed. Gravitational forces collapsed these clouds to form stars, such as those shown in the upper center of the illustration. These stars converted hydrogen and helium into heavier elements, including those such as carbon, nitrogen, and oxygen, which are necessary for life. These elements were returned to interstellar space by explosions of some of these stars to form clouds (note nebula in illustration) in which simple molecules such as water, carbon monoxide, and hydrocarbons were formed. These clouds then collapsed to form a new generation of stars and solar systems. In at least one solar system, our own, a variety of objects were formed, including comets (believed to be the most primitive objects in our solar system), meteorites, asteroids, and planets (represented by Saturn in the illustration). One of the planets, the Earth, formed at a distance from the sun where conditions were favorable and the necessary chemical ingredients were available (note illustration's infalling comet and dust) for the origin of life.

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

The Prebiotic Earth

The final, most important events leading to the origin of life are perhaps the least understood chapters of the story. Life began during the first billion years of an Earth history which is 4.5 billion years old. The illustration depicts an early Earth in which volcanoes, a gray, lifeless ocean, and a turbulent atmosphere dominated the landscape. Vigorous chemical activity is represented by the heavy clouds, which were fed by volcanoes and penetrated both by lightning discharges and solar radiation. The ocean received organic matter from the land and the atmosphere, as well as from infalling meteorites and comets. Here, substances such as water, carbon dioxide, methane, and hydrogen cyanide formed key molecules such as sugars, amino acids, and nucleotides. Such molecules are the building blocks of proteins and nucleic acids, compounds ubiquitous to all living organisms. A critical early triumph was the development of RNA and DNA molecules, which directed biological processes and preserved life's "operation instructions" for future generations. RNA and DNA are depicted in the illustration, first as fragmets and then as fully assembled helices. These helices formed some of the living threads, as shown in the illustration, however, other threads derived from planetary processes such as ocean chemistry and volcanic activity. This evolving bundle of threads thus arose from a variety of sources, illustrating that the origin of life was triggered not only by special molecules such as RNA or DNA, but also by the chemical and physical properties of the Earth's primitive environments.

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

The Prebiotic Earth

Most of life's history involved the biochemical evolution of single-celled microorganisms. We find individual fossilized microbes in rocks 3.5 billion years old, yet we can conclusively identify multicelled fossils only in rocks younger than 1 billion years. The oldest microbial communities often constructed layered mound-shaped deposits called stromatolites, whose structures suggest that those organisms sought light and were therefore photosynthetic. These early stromatolites grew along ancient seacoasts and endured harsh sunlight as well as episodic wetting and drying by tides. Thus it appears that, even as early as 3.5 billion years ago, microorganisms had become remarkably durable and sophisticated!

Many important events mark the interval between 1 and 3 billion years ago. As the illustration shows, smaller volcanic terrains were joined by larger, more stable granitic continents. Life learned how to release oxygen from water, and it populated the newly expanded continental shelf regions. The illustration depicts these events, both in the abundant mound-shaped stromatolites along the shoreline and in the greater variety of filamentous and spherical microbes in the foreground. Finally, between 1 and 2 billion years ago, the eukaryotic cells with their complex system of organells and membranes developed (note the euglena in the illustration) and began to experiment with multicelled body structures. The illustration shows a primitive jellyfish and two Ediacarian "sea pens."

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

The Prebiotic Earth

The evolution of the plants and animals most familiar to us occurred only in the last 550 million years. The illustration depicts the appearance of marine invertebrates (such as shell-making ammonites), then fish, amphibians, reptiles, mammals, and humanity. The life thread which continues on in the oceans to the right reminds us that the evolution of aquatic life continues even today. The development of land plant communities is also depicted, showing he relatively ancient clubmosses, horsetails, and ferns, and the more recent gymnosperms (for example, conifers) and angiosperms (flowering plants).

Perhaps the most recent significant evolutionary innovation has been humanity's ability to record and build upon its experience, thus triggering the rise of civilization and technology. These developments bring us to the present, and, as the thread of life reaches the summit of a tree-covered hill, we ponder our future.

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

Evolution of the Cosmos

Given the huge number of stars known to exist in the universe, life has very likely also developed elsewhere. If this "other" life can control and transmit energy such as light and radio waves, we just might be able to detect it.

As Space Agences develop their missions to build a space station and to visit other solar system bodies such as comets, planets, and moons, it responds to humanity's need to return to the cosmos, both to understand life's origins as well as to expand its horizons.

http://cmex-www.arc.nasa.gov/VikingCD/Puzzle/EvoLife.htm


Evolutionary genetics

Molecular clock

The molecular clock (based on the molecular clock hypothesis – MCH) is a technique in genetics, which researchers use to date when two species diverged, deduces elapsed time from the number of minor differences between their DNA sequences.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Molecular clock

The notion of a "molecular clock" was first attributed to Emile Zuckerkandl and Linus Pauling who, in 1962, noticed that the quantity of amino acid differences in hemoglobin between lineages roughly matched the known evolutionary rate of divergence based upon fossil evidence.

They generalized this observation to assert that the rate of evolutionary change of any specified protein was approximately constant over time and over different lineages.

It has been applied to DNA sequence evolution also, particularly neutral evolution.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Molecular clock

Allan Wilson and Vince Sarich built upon this work and the work of Motoo Kimura (1968) observed and formailized that rare spontaneous errors in DNA replication cause the mutations that drive molecular evolution, and that the accumulation of evolutionarily "neutral" differences between two sequences could be used to measure time, if the error rate of DNA replication could be calibrated. One method of calibrating the error rate was to use as references pairs of groups of living species whose date of speciation was already known from the fossil record.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Molecular clock

Originally, it was assumed that the DNA replication error rate was constant--not just over time, but across all species and every part of a genome that you might want to compare. Because the enzymes that replicate DNA differ only very slightly between species, the assumption seemed reasonable a priori. As molecular evidence has accumulated, the constant-rate assumption has proven false--or at least overly general. However while the MCH canot be blindly assumed to be true, it does hold in many cases, and these can be tested for. For example, molecular clock users are developing workaround solutions using a number of statistical approaches including maximum likelihood techniques and later Bayesian modeling.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Molecular clock

The molecular clock technique is an important tool in molecular systematics, the use of molecular genetics information to determine the correct scientific classification of organisms. Knowledge of approximately-constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of phylogenetic events.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

The neutral theory of molecular evolution (also, simply the neutral theory of evolution) is an influential theory that was introduced with provocative effect by Motoo Kimura in the late 1960s and early 1970s. Although the theory was received by some as an argument against Darwin's theory of evolution by natural selection, Kimura and most evolutionary biologists today maintain that the two theories are compatible. The theory attributes a large role to genetic drift.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

According to Kimura, when one compares the genomes of existing species, the vast majority of single-nucleotide differences are selectively "neutral." That is, these differences do not influence the fitness of either the species or the individuals who make up the species. As a result, the theory regards these genome features as neither subject to, nor explicable by, natural selection. This view is based in part on the genetic code, according to which sequences of three nucleotides (codons) may differ and yet encode the same amino acid (GCC and GCA both encode alanine, for example). Consequently, many potential single-nucleotide changes are in effect "silent" or "unexpressed" (see synonymous or silent substitution). Such changes are presumed to have little or no biological effect.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

A second assertion or hypothesis of the neutral theory is that most evolutionary change is the result of genetic drift acting on neutral alleles. A new allele arises typically through the spontaneous mutation of a single nucleotide within the sequence of a gene. In single-celled organisms, such an event immediately contributes a new allele to the population, and this allele is subject to drift. In sexually reproducing, multicellular organisms, the nucleotide substitution must arise within one of the many sex cells that an individual carries. Then only if that sex cell participates in the genesis of an embryo and offspring does the mutation contribute a new allele to the population. Neutral substitutions create new neutral alleles.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

Through drift, these new alleles may become more common within the population. They may subsequently decline and disappear, or in rare cases they may become "fixed"--meaning that the substitution they carry becomes a universal feature of the population or species. When an allele carrying one of these new substitutions becomes fixed, the effect is to add a substitution to the sequence of the previously fixed allele. In this way, neutral substitutions tend to accumulate, and genomes tend to evolve.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

According to the mathematics of drift, when looking between two species or two isolated populations, most of their single-nucleotide differences can be assumed to have accumulated at the same rate as individuals with mutations are born. This latter rate, it has been argued, is predictable from the error rate of the enzymes that carry out DNA replication--enzymes that have been well studied and are highly conserved across all species. Thus, the neutral theory is the foundation of the molecular clock technique, which evolutionary molecular biologists use to measure how much time has passed since species diverged from a common ancestor. While the mutation rate is no longer considered a constant, diverse and more sophisticated clock techniques have emerged.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

Neutral theory of molecular evolution

Many molecular biologists and population geneticists, besides Kimura, contributed to the development of the neutral theory, which may be viewed as an offshoot of the modern evolutionary synthesis.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

The "neutralist-selectionist" debate

A heated debate arose on the initial publication of Kimura's theory, in which discussion largely revolved around the relative percentages of alleles that are "neutral" versus "non-neutral" in any given genome. Contrary to the perception of many onlookers, the debate was not about whether or not natural selection acts at all.

Tomoko Ohta extended the neutral theory to include the concept of "near-neutrality", that is, genes that are affected mostly by drift or mostly by selection depending on the effective size of a breeding population. The neutralist-selectionist quarrel has since cooled, yet the question of the relative percentages of neutral and non-neutral alleles remains.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Modern concepts of evolution

The "neutralist-selectionist" debate

As of the early 2000s, the neutral theory is widely used as a "null model" for so-called null hypothesis testing. Researchers typically apply such a test when they aready have an estimate of the amount of time that has passed since two species or lineages diverged--for example, from radiocarbon dating at fossil excavation sites, or from historical records in the case of human families. The test compares the actual number of differences between two sequences and the number that the neutral theory predicts given the independently estimated divergence time. If the actual number of differences is much less than the prediction, the null hypothesis has failed, and researchers may reasonably assume that selection has acted on the sequences in question. Thus such tests contribute to the ongoing investigation into the extent to which molecular evolution is neutral.

http://en.wikipedia.org/wiki/Main_Page


Evolutionary genetics

Evolutionary history

of Homo sapiens

1. MULTIREGIONAL HYPOTHESIS

  • Based on morphology of fossil specimens

  • Archaic sapiens spread out of Africa to Europe and Asia.

  • All three populations evolved into modern sapiens .

  • Gene flow spread modern traits among the various populations

  • No reproductive isolation between ancient and modern sapiens

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

2. REPLACEMENT (OUT OF AFRICA) HYPOTHESIS

  • Archaic sapiens spread out of Africa to Europe and Asia.

  • Modern sapiens evolved from ancient sapiens in Africa.

  • Modern sapiens spread throughout the world in a 2nd expansion

  • Modern sapiens replaced ancient sapiens in Europe and Asia without interbreeding to any substantial extent because of reproductive isolation between ancient and modern forms

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

The MULTIREGIONAL and REPLACEMENT hypotheses make different predictions about the form of human gene trees

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

Predictions of the MULTIREGIONAL HYPOTHESIS: The gene geneology should have a long history of divergence and hence differ by many nucleotide substitutions Predictions of the

REPLACEMENT HYPOTHESIS: The gene geneology should be shallower with fewer nucleotide substitutions among haplotypes because of their recent common ancestry

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

The evidence from molecular data are:

One of the first molecular studies (Cann et al. 1987) used sequence divergence in mitochondrial DNA (mtDNA).

They showed that a mtDNA gene tree coalesced to a single ancestral gene copy between 160,000 and 249,000 MYA.

This gene tree implied that the ancestral sequence came from an African population

The results were challenged when it was found that the phylogenetic tree presented was only one of many equally parsimonious trees, some of which coalesced to more ancient times

Some, more recent studies, are also consistent with replacement hypothesis, but others support the multiregional hypothesis.

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

MIGRATIONS OF HUMAN POPULATIONS

Allele frequencies at various loci have been used to try and trace the spread of human genes to different geographic areas. These provide insights into the history of modern human populations

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Evolutionary history

of Homo sapiens

MIGRATIONS OF HUMAN POPULATIONS

http://www.wordiq.com/definition/Out_of_Africa_hypothesis


Evolutionary genetics

Evolutionary history

of Homo sapiens

MIGRATIONS OF HUMAN POPULATIONS

  • SUMMARY

  • Cavalli Sforza et al. (1994) suggest that modern humans spread:

  • from Africa to S. Asia

  • from S. Asia to Australia and Northern Asia

  • a. from N. Asia populations spread into Europe (about the same time that Neanderthal archaic sapiens disappeared)

  • b. from N. Asia populations spread into the Americas via the Bering land bridge that connected Siberia with Alaska

http://eebweb.arizona.edu/courses/Ecol435_535/Dec2.htm


Evolutionary genetics

Map of human genetic diversity,from the dust jacket of

The History and Geography of Human Genes, 1994

Luigi Luca Cavalli-Sforza


Evolutionary genetics

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