Glossary - boxes from the book
Adaptive radiation is rapidly repeated speciation of the species of a particular evolutionary line. It has at least two different reasons. The first cause is the penetration of the representatives of a particular line into an environment that has many utilizable but, at the given time, unutilized resources. A species that enters such an environment in that, for example, it reaches an island, “learns” to utilize the individual resources and diversifies into a great many species through gradual adaptation to the individual types of resources and individual types of environment. The second cause of evolutionary radiation is the formation of fundamentally new features that, for some reason, open a broader range of so-far unused niches for their carriers. For example, the formation of wings and the ability to fly enables the particular group of vertebrates to utilize various types of resources with scattered occurrence over a large territory. As a consequence, thousands of species of birds could evolve relatively rapidly, using various types of resources as food, from seeds and fruit through insects, to vertebrates.
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Organisms exhibit a vast number of properties (organs and patterns of behaviour) that assist in their successful survival and reproduction. Some organs assisting in successful survival are quite simple and their usefulness and means of evolution are easy to discover (fins for swimming, parachutes on dandelion seeds for dispersion), while others are highly ingenious. For example, some kinds of orchids (Ophrys) have a structure in their flowers whose shape, colour and scent are similar to the females of a certain kind of fly. Thus, males are attracted to the flowers and attempt to copulate with the dummy female and thus transfer pollen from one flower to the next. Tobacco and cotton plants can recognize that they are being eaten by the caterpillars of the moth Heliothis virescens (tobacco budworm) (they can even distinguish that they are being damaged by this pest and not the caterpillars of some other kind of moth or a scientist punching holes in the leaves). In order to get rid of the intruder (or at least to make his life harder), they begin to emit chemical substances that attract the natural enemies of this kind of caterpillar, the parasitoid wasp Cardiochiles nigriceps, which lays eggs in the caterpillar. These parasitoid wasps fly to the plants even if the scientist first removes the caterpillars and the damaged leaf. The plants do, of course, not know that they are doing this – in this sense, it is not truly goal-oriented behaviour. However, it is certainly useful behaviour as it truly effectively assists the plant to get rid of the particular species of pest.
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A variant of a gene, differing from other variants of this gene in its manifestation, is called an allele. One variant of the gene can be responsible for brown eyes and another for blue eyes. I would probably manage to write the book without the term “allele”, and could use the term “gene variant” instead. But my colleagues who might happen to read the book would laugh at me, saying that I have lost my memory for even the most basic genetic terminology (and they wouldn’t be that far from the truth), or they would not be sure whether I were speaking of alleles or of something else. So I guess you have no choice but to get used to the term “allele” (and the term “phenotype”, see Phenotype). At least at the beginning, I will give both possibilities (allele and gene variant), so I am sure we will manage it. After reading the book, you can surprise your friends with your newly acquired knowledge (or throw them off balance – which is also okay).
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Autosomes are all the chromosomes with the exception of sex chromosomes. While Y chromosomes occur in each generation only in the bodies of males and X chromosomes spend twice as much time in the bodies of females than in the bodies of males (because there are two copies in each cell), autosomes occur with the same frequency in males and females.
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This term refers to biological diversity – heterogeneity. This has two components, on the one hand diversity in the narrow sense, which is the number of species and, on the other hand, disparity, which is the number of body plans of organisms and their difference. We can speak of local biodiversity, i.e. the diversity and disparity of species occurring in a particular territory or in a certain kind of habitat, and of global diversity, i.e. diversity and disparity of all the organisms on the Earth.
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Biogeography is a science that is concerned with the study of the laws (and specificities) of the distribution of the individual species of organisms and the individual groups of organisms on the Earth. The presence or absence of species in a certain territory is explained in terms of differences in local conditions, the manner of migration (relocation in space from generation to generation) of the members of the individual species, changes in the spatial distribution of land on the globe and adaptive radiation of species at a particular site.
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This was originally an umbrella term expressing the overall ability of an individual to produce (fertile) descendants in comparison with the other members of the population. Neodarwinists assign biological fitness to individual alleles. In this conception, this is a number that expresses how many fewer descendants on average are produced during its lifetime by the carrier of a particular allele compared to the carriers of the most successful alleles in the particular population. The biological fitness (w) can be used to calculate a selection coefficient (s) as w = 1 – s. The selection coefficient is thus the obverse of biological fitness as it expresses the degree to which the bearers of certain alleles are affected by natural selection. If the carriers of allele A on an average leave the greatest number of descendants, i.e. 10, while the carriers of allele B leave an average of 8 descendants, then the biological fitness of carriers of allele B is 0.8 and the corresponding selection coefficient is 0.2.
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This is a set of rules and formal procedures using which we can derive the truth or untruth of a complicated statement consisting of a number of individual (true or untrue) statements. The individual statements are connected together by the logical operators AND, OR, XOR or the derived operator NOT. The logical operation AND yields the output TRUE if both the input statements are true. For example, the statement “It is snowing and raining outside” is true only if both individual statements are true, i.e. when it is raining and also snowing outside. The logical operation OR yields the output TRUE if at least one of the individual statements is true. For example, the statement “It is snowing or raining outside” is true if at least one of the individual statements is true, i.e. if it is raining outside or if it is snowing outside or if it is raining and snowing outside. The statement XOR is true only if one of the individual statements is true, i.e. it is raining outside or it is snowing outside, but it would not be true if it were both snowing and raining. If an (individual or complex) statement is introduced by the operator NOT, its validity is negated (a true statement becomes untrue and vice versa).
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Cells are the basic living units of all contemporary organisms with the exception of viruses. In some species of organisms, the body consists of a single cell (single-cell organisms); in other species, i.e. multi-cellular organisms, the cells multiply repeatedly during ontogeny, are variously relocated and diversify until, compared with the microscopic cells, they form the enormous bodies of a multi-cellular organism. The human body is apparently formed of about 50 trillion (i.e. 5 × 1013) cells.
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We will leave the question of whether chance exists objectively, or whether all events occur according to certain laws, to philosophers. However, subjectively, chance certainly exists. We consider that all events, whose occurrence does not follow from the properties of the system that is the subject of our interest and whose behaviour we wish to explain, are governed by chance. For example, the extinction of the dinosaurs at the end of the Mesosoic as a consequence of the impact of a cosmic body was a chance event from the standpoint of a biologist, as it was not possible to derive in any way that it would occur from the properties of the organisms that occurred at that time on the Earth and from the laws governing the development of living systems. Simultaneously, it is of no importance whether or not it was determined at the instant of formation of the solar system that this cosmic projectile would collide with the Earth and thus whether it was or was not possible to predict that this would occur from knowledge of the positions and movements of the bodies of the solar system (and its surroundings) and on the basis of the laws of physics.
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Genetic information is written in the DNA molecule in the cells (see DNA). Human DNA in the cell nucleus has an overall length of about two metres. In order for it to fit into the cell, it is wound around specialized proteins (histones) and, together with them, folded many times and wound in chromosomes, rod-like shapes usually with a length of several thousandths of a millimetre. For example, human beings have 46 of these species, which differ in size and shape, in the cell nucleus. Each chromosome is formed of two identical chromatids, whose DNA was formed by copying the chain of a DNA molecule originally contained in one chromatid (Fig. 3.1 in the book). During nuclear division, the two chromatids separate to the opposite ends of the cell, ensuring fair (even) distribution of the genetic material between the two daughter cells. When cells are not dividing, the chromosomes are loosened and are not visible without using special microscope techniques. They change into their characteristic form observable under a normal (optical) microscope during cell division.
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Continental and oceanic islands
In the past, some islands (continental islands) formed part of the mainland (or of the continental shelf), from which they either became separated when the sea level rose (British Isles) or crumbled off the edges when the continental blocks rifted (some of the Seychelles). Some islands are so large and geologically old that they basically form small continents (New Guinea). Distinctive fauna and flora occur on all types of islands, frequently including species whose relatives have become extinct on the parent mainland. From the standpoint of study of evolutionary plasticity, however, oceanic islands located far away from the mainland are important; these were formed, e.g., as a result of volcanic activity or a combination of volcanoes and corral reefs, and were colonized in the past only by individual “shipwrecked” species arriving from the distant mainland (Hawaiian Islands). Only these species underwent a dramatic decrease in the population size that could renew their evolutionary plasticity.
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Determination of phylogenesis
The most important method of determining phylogenesis is based on gradual connecting of species that share new evolutionary features, called apomorphic traits (the opposite of an apomorphic trait is a plesiomorphic trait – the original evolutionary form of the trait). Traits that are so complicated that it can be assumed that they were formed in evolution only once and that species that share them did not form the trait independently, but inherited them from a joint predecessor, can be considered to be useful apomorphic traits for phylogenetics. If two species A and B share ten apomorphic traits, but share only seven apomorphic traits with a third species C, it can be assumed that species A and B branched off from a joint predecessor in evolution later than that predecessor from the species that was also a predecessor of species C.
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DNA molecules are fundamentally like two long strings of beads, each of which consists in irregular alternation of four types of beads – nucleotides, twisted in a helix, one around the other (Fig. 3.2 in the book). At the site where nucleotide A is present in one chain, nucleotide T is present in the second chain and where nucleotide G is present in one chain, nucleotide C is present in the other chain. If the two chains are separated, which can be achieved, e.g., by heating, the appropriate enzyme and all four nucleotides and a few other things are added, the appropriate complementary chain is formed according to the sequence in each chain so that, finally, instead of one DNA double chain, two identical DNA double chains are obtained (Fig. 3.3 in the book). This is essentially the basis for heredity of genetic information.
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Do psychological factors or genes determine human behaviour?
Basically, actually genes – although rarely in that they would directly affect our conscious and subconscious processes of evaluating information and thus determine our behaviour. However, they controlled the creation of our bodies, including our brains, and thus predetermined how our brains will respond to various stimuli that come to them through our senses. The traditional differentiation of nature vs. nurture is thus, basically, artificial – the behaviour of people is mostly determined by what they learn, i.e. culture; however, what we learn is predetermined by our genes.
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A niche is a simple term for the life style of a particular species, the manner in which it utilizes the resources in its environment (sources of food and also shelter from predators), how much it is harmed by the individual physical, chemical or biological factors of the environment. The niches of various species can partly overlap; however, two species that have completely overlapping niches cannot survive for long in the same place. In addition, there is a negligibly small chance that two species will have exactly the same niches. Ecologists are divided into two groups with different opinions. Part of them state that first the species is created and that the term “empty niche” doesn’t have any meaning. Another group of ecologists are of the opinion that an empty (unoccupied) niche is a logically incorrect term but simultaneously easy to understand intuitively and highly necessary.
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Eukaryotic and prokaryotic organisms
The original organisms occurring on the Earth were prokaryotic, i.e. their cells did not have a classical nucleus and a number of other organelles. Of contemporary organisms, two groups, bacteria and the less well known archaea, are prokaryotes. Eukaryotes developed much later from prokaryotes. They have much larger cells, in typical cases their volume is greater by 3–4 orders of magnitude; they contain a nuclear cell wrapped in a double membrane and a number of specialized organelles, of which some, specifically mitochondria and chloroplasts, were formed at some time in the past by “taming” prokaryotic organisms – possibly parasitic bacteria related to present-day rickettsia (mitochondria) and algae (chloroplasts). A eukaryotic cell is actually a sort of conglomerate (chimera), formed in the past by the combination of several prokaryotic organisms belonging to both the group of archaea and the group of bacteria. For this reason, mitochondria and chloroplasts continue to bear their own genome – residues of the DNA of the original symbiont. In the framework of eukaryotic organisms, multicellular organisms developed over time, for example plants and animals. Prokaryotic organisms remained single-celled, but frequently form colonies of cooperating cells (belonging to a single species or to several species).
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Evolution is generally understood to mean gradual development of any system with a “memory”, i.e. any system that responds to external stimuli in dependence on the stimuli that it encountered in the past. This means that it is equally possible to speak of the evolution of languages, automobile chasses or ladies’ hairstyles as about the evolution of conifers. Evolution can be direct, reverse or cyclic. Biological evolution is one of the many types of evolution. It is interesting primarily in that organisms are formed spontaneously during this process, i.e. systems that are usefully adapted to the use of various resources in the environment, including such marvellous creatures as fruit flies, coconut palms, sturgeons and the readers of this book.
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Exponential and linear growth
If the population in each generation increases by a constant multiple and if, for example, it doubles in each generation, this is called exponential growth. Exponential growth is constantly faster – if there are ten individuals in the first generation, there will be twenty in the second, forty in the third, eighty in the fourth, etc. In contrast, linear growth occurs when the number increases by a constant amount in each generation, e.g. by 10 individuals. Linear growth occurs at a constant rate – if there are ten individuals in the first generation, there will be twenty in the second, thirty in the third, forty in the fourth, etc.
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Extinction of species
At the present time, the extinction of a species is considered to be the instant when the last representative of the particular species dies. “Pseudo-extinction”, i.e. the gradual change of one species into a different species, is not considered to constitute extinction; some palaeontologists believe in the existence of this process that, according to the theory of frozen plasticity, should occur only in asexually reproducing species. Palaeontological data indicate that extinction is the unavoidable fate of every species. The average time of survival of species differs for the individual taxons. For example, the period of survival of the average mammal species varies around 5 million years, while the period of survival of sea snails and clams is about 10–20 million years. Species become extinct, either as a consequence of sudden catastrophic events, for example the impact of asteroids or the cores of comets on the Earth, or gradually, as if there were no external cause at all. Some facts indicate that the commonest cause of gradual (called background) extinction consists in pandemics caused by a parasite, probably most frequently a virus, see also Footnote 3 in Chapter 16 of the book.
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Frequency-dependent selection and left-handed people
According to some authors, the frequency of left-handed people in the population is regulated by frequency-dependent selection. Left-handed people are at an advantage in battles and fist-fights (and also in a number of sports) as their opponents are not prepared for their fighting methods because there are fewer of them in the population than right-handed people. Comparative studies on a large number of traditional human populations have actually shown that that the frequency of left-handed people (3–27%) is directly dependent on the amount of violence in the population (specifically, the number of violent deaths).
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The name of the ancient Greek goddess Gaia is used to denote the hypothetical superorganism consisting of the entire biosphere of the planet Earth. As the presence of various homeostatic mechanisms is typical for organisms, maintaining their individual body parameters (temperature, chemical composition, etc.) within the physiological boundaries required for the life of the organism, similarly, in the biosphere of the Earth, we can find a great many regulation mechanisms maintaining various physical and chemical conditions predominating on the Earth within boundaries compatible with survival of the individual species. It is only thanks to the activities of living organisms that, for example, the temperature of the surface of the Earth remains constant over long periods of time, regardless of the fact that the amount of light from the sun and thus the input of energy has increased substantially over the past 4 billion years. Similarly, the activities of organisms regulate the level of oxygen and carbon dioxide in the atmosphere. In the absence of life, the conditions on Earth would have become similar to those on Mars long ago. The activities of organisms are greatly affected and frequently even directly determined by the individual geological processes occurring in the Earth’s crust, from the processes of weathering to possibly as far as the movements of the continents caused by continental drift.
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This is an area of applied mathematics that attempts to analyze the progress and results of the competition of individuals that utilize different strategies to maximize their returns. Game theory indicates that the success of individual strategies is frequently dependent on their representation in the population. Some strategies that are very successful when rare can be very unsuccessful when used more frequently.
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This is one of the basic concepts of modern biology designating the predisposition for certain traits. However, even professionals in various fields cannot agree on a specific meaning for the word gene. Molecular geneticists have a clear concept in this respect as they define a gene as a continuous segment of a DNA molecule. Evolutionary biologists know this is ridiculous and that a gene cannot be defined in this way, but they are in a negligible minority at the present time and, if they were to fight for their version of the truth, they would definitely suffer defeat. Consequently, they prefer to grit their teeth in silence and act as if everything were fine (and usually alternately use the concept of a gene in the original and in the molecular biological meaning). In this entire book, the concept of gene could be replaced by the word predisposition. The reason why I don’t satisfy non-biologist readers and why I don’t replace it by the word predisposition lies primarily in the fact that I will also have to use other technical terms that are derived from the word gene. These include genotype, genome and gene pool. Predispositiontype, predispositionome, predisposition pool – no I guess that wouldn’t work.
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Genetic interaction is the dependence of the degree or character of the manifestation of one allele on the presence of other alleles. If these are alleles of a single gene, only several basic possibilities can occur in diploid organisms that bear two alleles from each gene. If allele A completely suppresses the manifestation of allele B and an individual with two A alleles then looks the same as an individual with one A allele and one B allele, then allele A is denoted as dominant with respect to allele B, while allele B is denoted as recessive with respect to allele A. For example, this is the case of the allele for brown and blue eye colour – a homozygote with two alleles for brown eye colour does not differ from a heterozygote that bears one allele for brown colour and one allele for blue colour (simplified somewhat – I hope experts will forgive me). If the expression of alleles A and B are averaged out and an individual with a pair of alleles AB (heterozygote) has traits somewhere between the traits of individuals with two A alleles and the traits of individuals with two B alleles, this is called semi-dominance (incomplete dominance) – the allele of the pair that is manifested more strongly in the heterozygote is denoted as semi-dominant. For example, semi-dominance is exhibited by the S allele responsible for the detrimental manifestations of sickle cell anemia – a homozygote with two alleles is much worse off than a heterozygote with one normal and one S allele. The case when a heterozygote with a pair of alleles AB exhibits the relevant trait to a greater degree than either homozygotes AA or BB is termed super-dominance. Only a limited number of types of gene interaction can occur between the alleles of a single gene in diploid organisms. There are a much greater number of types of gene interactions between the alleles of various genes, called epistatic interactions, because the number of interacting alleles can attain any number. For example, a particular allele of one gene can directly affect the manifestations of alleles A and B of a different gene and can also affect whether allele A will be dominant or recessive towards allele B.
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The strength of the genetic linkage measures the probability with which recombination will occur between two genes on a chromosome. This is determined by the distance between the location of the particular genes on the chromosome and also the frequency of recombination at the given site on the chromosome. The existence of a genetic linkage is the reason why the behaviour of many pairs of genes is not governed by Mendel’s second law, i.e. the law of independent combinability of predispositions. The strength of a genetic linkage can be measured from the ratio of the number of descendants in which recombination occurred between the particular genes and the number of descendants without recombination in this section. If there is the same number of both types of individuals in the progeny (for example, if the genes are located on different chromosomes), the genetic bond is zero; however, if the genes are close together on the same chromosome or if recombination does not occur in the area between the genes for some reason, the bond between the genes can be practically absolute.
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Genetic recombination and segregation
These are processes that occur during the formation of sex cells. In these processes, a pair of similar, i.e. homologous, chromosomes in the nucleus forms doublets and mutually recombine. In recombination, the DNA molecule is broken at the same place in both homologous chromosomes. If the original parts of the same chromosome subsequently rejoin, no recombination occurs; however, if a strand of one chromosome joins together with a strand from the second chromosome, the pair of recombined chromosomes will differ in the combination of their alleles from the two original chromosomes. While, prior to recombination, it was possible to state that one chromosome was derived from the father and one from the mother, the recombined chromosomes contain part of the alleles from the father and part from the mother. Segregation occurs during the separation of homologous chromosomes to the opposite ends of dividing cells. In this process, one of the chromosomes of each pair moves quite randomly to the opposite end of the cell. Even if recombination did not occur before this, the segregation of the chromosomes of paternal and maternal origin would give the newly formed cells their own combination of paternal and maternal alleles, different from the combination of alleles of either of its parents. Following separation of the pair of chromosomes in the first meiotic division, the two sister chromatids of each chromosome separate in the second meiotic division. Thus, four sex cells, haploid cells, can be formed from one diploid cell.
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Genome is the sum of all the genes occurring in the cells of a given individual. In contrast, genotype is the sum of all the alleles of a particular individual. The nuclear genome is the sum of all the genes occurring in the nucleus of the cell; the cytoplasmic or organelle genome is the sum of the genes contained in the DNA of cell organelles, mitochondria or plastids. The genomes of males and females of a certain species can differ in the presence or number of sex chromosomes, i.e. chromosomes whose occurrence or number determines whether the individual will develop as a male or female, see Y Chromosome.
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Genotype is a combination of alleles (gene variants) borne by a specific individual in his cells (cell – see Cells). In diploid organisms, each individual has a pair of alleles from each gene in his cells, where this can be a pair of identical alleles (homozygote) or a pair of different alleles (heterozygote). Because the number of genes in the genome (see Genome) of organisms is enormous and a large percent of them occur in many variants in a given species, the number of possible combinations of alleles – number of different genotypes – is unimaginably large and practically no pair of individuals in the population of a sexually reproducing species, with the exception of identical twins, has an identical genotype.
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Hard and soft heredity
Hard heredity consists in the transfer of the predispositions for individual traits from one generation to the next in unaltered form, without any effect on the other predispositions present in a particular individual and the effects of the external environment. In contrast, soft heredity assumes that predispositions can change from one generation to the next under the effect of the other predispositions present in a given individual and through the effect of the external environment. The Lamarckist theory of evolution and the later Darwin’s theory of evolution are based on the concept of soft heredity of predispositions; in contrast, the Neodarwinist theory of evolution, i.e. the main direction of the theory of evolutionary biology developed roughly from the 1930s and thus including the knowledge of Mendelian genetics, is based on the concepts of hard heredity.
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Heredity and heritability of traits
Heredity is the ability of traits (certain properties that adopt at least two forms in the population) to be inherited from parents by their offspring. Heritability of traits expresses the degree to which a certain trait is inherited from parents by progeny. The heritability of traits can be expressed as the fraction of genetically determined variability in the given trait in the total (i.e. determined genetically and through the effect of the external environment) variability of this trait.
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Island gigantism and nanism (dwarfism)
On islands, it occurs relatively frequently that large species of animals tend to get smaller and small species tend to get larger. The usual evolutionary explanation is that, on the mainland, the greater interspecies competition or pressure of carnivores forces them beyond the limits of their optimum size, i.e. all their members tend to be large, so that they can better resist carnivores, or small, so that they can hide better and manage with a small amount of available resources. When they reach an island, where their natural enemies or competitors are absent, they can return to their optimum size – i.e. get larger or smaller to the size at which their body functions best. This could be the right explanation. However, it is necessary to consider that not every change in body structure that we encounter on islands has the nature of gigantism or nanism and, in addition, a great many long-term isolated populations in areas with low intensity of inter-species competition are apparently also formed on the mainland (however, mostly by splitting off of part of a large population), without gigantic or dwarf forms occurring to the same degree as on islands.
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Lamarkian model of evolution
This model of evolution assumes that the adaptive traits of modern organisms are formed in that the members of a certain species begin to devote themselves to certain activities, for example, they reach the tops of trees for leaves, in this “exercise” they lengthen their necks and their offspring then inherit these prolonged necks. It cannot now be determined whether Lamarck really had such a naïve idea, he did not state things so explicitly in his work “Philosophia Zoologica”. That is, however, not important today – Lamarckism is now understood as the formation of adaptive traits through the relevant “exercising” and subsequent inheritance of these acquired properties.
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According to the manipulation hypothesis, a number of parasites purposefully and specifically alter the behaviour of their hosts and thus increase the probability of their transmission to an uninfected host. For example, it is assumed that toxoplasmosis can reduce fear of cats in infected rodents, or reduce the speed with which they can react to simple stimuli. Parasites transmitted by sexual intercourse could increase the sexual activity of their hosts or the attractiveness of infected males for females. In some cases, parasites affect the behaviour of their hosts directly, e.g. by targeted interventions into the nervous system (rabies), in some cases indirectly; for example, the bacteria causing the plague damage the oral system of fleas so that they can bite, but cannot suck blood, an infected flea is therefore constantly hungry and bites and thus infects more hosts.
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Mendel’s laws of genetics
According to Mendel’s first law (the law of segregation), in each generation, two alleles of any gene present in the parent individual segregate into independent sex cells (e.g. into individual sperm) without undergoing any change and without affecting one another. The second law (the law of independent assortment of characters) states that the individual pairs of alleles of various genes segregate into sex cells independently of one another and that the manner of segregation of one pair of alleles in no way affects the segregation of another pair. In the first decades of the 20th century, geneticists demonstrated that Mendel’s second law applies only to pairs of genes, each of which belongs to a different chromosome (see also Why do elephants change faster than mice?).
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Microevolution and macroevolution
Evolutionary processes that tend to occur at a population level are considered to be microevolutionary, while evolutionary processes (the formation and disappearance of the large branches of the phylogenetic tree, the formation of new body plans) that occur at the level of species can be considered to constitute macroevolution. Macroevolutionary processes are slow and prolonged and it is hardly possible for us to study them in our experiments. The element of chance plays a much greater role in them than in microevolutionary processes, see Chapter 4 in the book. The main source of evolutionary novelties in macroevolution consists in mutations arising in a local population, while the main source of novelties in microevolution is gene flow – the arrival of new alleles in the population through migrants.
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Model of punctuated equilibria
Eldredge and Gould called their discovery the “Model of punctuated equilibria”. The name is intended to express their concept that evolution occurs as an alternation of short periods of tumultuous change followed by a long period of evolutionary calm (stasis). Thus evolution is not gradualistic, occurring as a slow, more or less regular change in shapes and functions and smooth transition of the older species into a new species, but rather punctuated, and is characterized by jerky development that occasionally occurs rapidly, but with long intervals when nothing at all happens. As I have discovered on extensive experimental material from students, punctuated evolution (in Czech punktuacionalistická evoluce) is a term that is impossible to remember or at least enunciate. Anyone who can say it rapidly three times in a row (in Czech) can consider himself to be an experienced evolutionary biologist and can, without trepidation, apply for the position of head of a department of evolutionary biology at any Czech university. (I have not managed yet, but that does not matter, because no Czech universities have a department of evolutionary biology.)
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Palaeontology and palaeontologists
In contrast to evolutionary biology, which is concerned with the general laws of the development of life, palaeontology is concerned with the specific history of the alternation of species on the Earth. The main source of palaeontological knowledge consists in fossils, ancient remains of the bodies of organisms (or rather their hard parts) or remains left by their activities (paths, faeces) that have escaped decomposition by happy circumstances and have remained in better or worse preserved form to the present day.
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This term denotes the combination of all the traits of an individual, including its behaviour. With a certain degree of simplification, it might be possible to use the word “appearance” instead of phenotype; however, it must be borne in mind that phenotype also includes internal properties, which are not visible externally, and also behaviour. Thus, it will probably be more practical to use the proper scientific term “phenotype”. At least the reader will be each time reminded that this is a technical scientific term, for which there is an exact definition and which all scientists use (or at least should use) in the same way. This is, incidentally, the reason why scientists use scientific, frequently Latin or Greek, expressions and why they don’t speak plain English. The meanings of words in normal language are not exactly defined and thus scientists could not discuss things unambiguously. “You said appearance, my colleague. Did you mean by this also the shape of the pancreas?”
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The phylogenetic tree, or phylogram, is a graphical representation of phylogenesis, the gradual divergence of species from a common ancestor. In addition to the order of divergence of the individual species, a time scale can also be designated on the phylogenetic tree, permitting dating of the individual events in phylogenesis. For some purposes, it is useful to denote changes in the properties of the studied organisms on the phylogenetic tree, termed anagenesis. If the graph is used to depict not genealogical relationships between organisms, but their mutual similarity, then this is called a phenogram. Mutually unrelated species living in a similar environment and exposed to similar selection pressures (fish, dolphins, sharks, ichthyosaurus) can gradually become more similar (i.e. converge to a similar body structure) and can be placed close to one another on a phenogram (but not on a phylogram).
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This is a statistical method that allows us to estimate the number of objects that must be studied in order to be able to statistically demonstrate a certain dependence. Basically, it can be stated that quite negligible and, from a practical standpoint, completely uninteresting dependences can be demonstrated in a sufficiently large set. For example, in order to demonstrate the effect of the shadowing of a field by flying swallows on the crop yield, all the arable land in Europe would probably have to be reserved for our “very important” study. Before a scientist decides to perform a more demanding study, he should first estimate, on the basis of the available information and using power analysis, how large a test set he will require to have a reasonable chance of demonstrating the studied effects. Power analysis simultaneously permits estimating post factum how far we can believe the results of a study that did not demonstrate the existence of the studied dependence.
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Quantitative and qualitative traits
Only very few of the traits that are exhibited by organisms are qualitative, i.e. have the nature of being “all or nothing”. The presence or absence of a certain mark on the surface of the body could be an example of such a trait. The size, intensity or colour of the mark, similarly to the size of the body and its parts, however, are quantitative traits, i.e. we can measure the intensity, size or, in relation to behaviour, the probability or frequency of its occurrence. While qualitative traits can be determined by the presence or absence of certain (frequently dysfunctional) alleles of one gene, quantitative traits are usually dependent on, or are at least affected by, a large number of genes located in various parts of the genome.
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Most known species existing on the Earth reproduce sexually. Members of a single species cross almost exclusively amongst themselves. They mostly do not cross with the members of other species, or at least their crossing does not yield progeny. Barriers preventing crossing between species and thus ensuring reproductive isolation are basically of two types, external and internal. External barriers are formed, e.g., by mountain ranges, which separate the areas of occurrence of the two species; internal barriers consist, e.g., in the number and shape of chromosomes, which differ in the two species and thus prevent meiotic division, necessary for the formation of sex cells, from progressing to its conclusion. In some cases, it is not easy to decide which type of barrier is involved. For example, most biologists would classify as an external barrier the incompatibility caused in many species of insects by infection of part of the population by parasitic bacteria of the Wolbachia genus, which is capable of preventing reproduction of an infected individual with an uninfected individual or an individual infected by a different strain of this bacteria. However, if the cause of the infection were a virus hiding directly in the DNA of the cell, most biologists would probably consider the resulting reproduction barrier to be an internal barrier.
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Rh negative and Rh positive persons
People can be divided into two groups, differing in the presence of certain forms of a protein on the surface of the red blood cells. Rh positive persons (about 80% of the European population) have the relevant molecule on their red blood cells, while this molecule is missing in Rh negative persons (in actual fact, it is usually there, but is altered – however, that is not important here). If the blood of an Rh positive person is transferred to the body of an Rh negative person, the appropriate antibody molecules are formed and destroy the blood cells derived from the Rh positive person. Transfer of blood from an Rh positive person can occur during organ transplants or naturally in Rh negative women who expect an Rh positive child (with an Rh positive father). In the past, the presence of these antibodies seriously affected the lives and health of subsequent children of the same woman.
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Selective pressure is pressure exerted by the environment or man on a certain population through removal of the bearer of certain traits, e.g. an above-average large or below-average small individual, or by preventing such an individual from reproducing. Selective pressure need not always mean a negative effect on the bearer of undesirable forms of the trait, but can just as well consist in support for individuals with the desirable form of the trait.
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Sexual and asexual organisms
To a first approximation, the situation is clear. Some species of organisms reproduce sexually, i.e. their descendants are formed by the merging of the sex cells of two organisms. Others reproduce asexually, i.e. their descendants are formed by splitting off of part of the parent organism (e.g. tubers for potatoes) or from individual specialized cells intended for this purpose (e.g. some species of stick insects and fish). On closer inspection, the location of the boundary between sexual and asexual reproduction is less clear and opinions of professionals on the difference between sexual and asexual reproduction need not completely agree. However, in this book, I will stick to the approach that considers asexual reproduction to be the formation of descendants with a genotype identical with that of one parent and sexual reproduction to be the formation of descendants with a genotype formed by the combination of the alleles of two parents. The fact that sexuality was almost certainly not originally connected with reproduction and fulfilled a completely different function is something I prefer to leave out here – this could even be the subject of a separate book.
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Stages in the development of evolutionary biology
Evolutionary theory based on Darwin’s texts, elaborated at approximately the beginning of the 1920s, is generally called Darwinism or Classical Darwinism. The theory of evolution that was formed by incorporation of knowledge of genetics into the Classical Darwinist theory is termed Neodarwinism. Neodarwinists primarily understand evolution as a change in the representation of the individual alleles in the gene pool of the population and attempt to explain all evolutionary processes occurring at the level within and between species on the basis of this process. Consequently, for this reason, chapters devoted to population genetics – learning about the development of the genetic composition of the population – take up considerable space in textbooks of evolutionary biology. For most biologists, we are still living in the era of Neodarwinism. According to others, especially the work of S.J. Gould, who sharply differentiate between microevolutionary processes, occurring at the level of populations and species, and macroevolutionary processes, occurring above the level of species, and the gene-centred models of evolution following from the work of W.D. Hamilton, see Chapter 8, a new era in evolutionary biology has already begun. With my characteristic malice, I would like to introduce the term Postneodarwinism for this approach (and I look forward to seeing how my successors will manage to find a name for the next era of evolutionary biology).
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For the natural scientist, statistics is primarily a set of mathematical procedures that allow him to search for laws in a world in which the element of chance is constantly in effect. Most frequently, the use of statistical methods consists in testing the validity of hypotheses. If, for example, we find that 20 students infected by the Toxoplasma protozoa are, on an average, taller than 72 uninfected students, the relevant statistical method allows us to estimate, on the basis of the heights of all the 92 students, the probability that the observed difference in the average height of the infected and uninfected students is only a matter of chance. In this case, the t-test told us that this probability equals only 2.6%, indicating that there is great probability that there is some dependence between the height of the students (men) and infection by Toxoplasma gondii. However, the results of statistical tests understandably cannot answer the question of whether the infection increases the growth of students or whether taller students have a greater probability of becoming infected by T. gondii or that the height of the students and the probability of infection are affected by a third factor. In this case, the suspicious joint factor that simultaneously affects the height of the students and the probability of infection is the level of testosterone.
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A taxon is a particular complete part of the phylogenetic tree (branch or monophyletic group or clade), which the relevant professional – taxonomist – defines and names. Thus, a taxon can be a single species, such as a chimpanzee, or perhaps the family of canine carnivores. At the present time, it is required that each taxon be monophyletic, i.e. that it include only a single species (common ancestor), whose ancestor was, itself, not a member of the particular taxon. A large number of experts (cladists) also require that the taxon include all the descendants of a particular common ancestor. Thus, cladists declared that a number of former taxons were invalid, including such ones as fish and reptiles. (It must be admitted that they had quite good reasons for this; however, it is probably better not to discuss this here.) A taxonomist can define and name any branch of the phylogenetic tree; however, in actual fact, he defines only those taxons whose members differ substantially in some way from the members of other taxons.
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The additive component of heritability
The heritability of traits is determined by the fraction of genetically determined variability in the given trait in the total variability of this trait, i.e. in the variability determined both genetically and nongenetically (by the effects of the external environment). Heritability in the narrow sense of the word expresses the fraction of the additive component of genetically determined variability in the total variability of the given trait. Additive variability is the component of the variability that is additive in its effects. If allele A of one gene acts, on an average, in its carriers to increase their body weight by 10% and allele B of another gene acts, on an average, in its carriers to increase their body weight by 5%, and if this is an additive component of the variability in both cases, then the carriers of alleles A and B will be, on an average, 15% larger than the carriers of other alleles. If this increase is smaller or greater than 15%, then nonadditive variability is involved.
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The effect of the parasite Toxoplasma gondii on the sex ratio of human beings
As mentioned in Chapter 2 in the book, many people are infected by the parasite Toxoplasma gondii throughout their lives. In developed countries, 15–40% of women of reproductive age are usually infected; in developing countries with lower hygienic standards, the occurrence of this “latent” toxoplasmosis approaches 90%. A study that we recently performed on a large number of women indicated that far more boys than girls are born to infected women in their first pregnancy. In a set of 111 women with the highest antibody levels (i.e. with the strongest or freshest, nonetheless latent, infection), the ratio of boys to girls attained a value of 2.6:1. We observed a similar phenomenon in experiments performed on infected mice. It is not yet known in which way toxoplasma affects the ratio of the sexes of human beings. However, it seems most probable that the protozoa in some way reduces the probability that the embryos of individuals of male sex will be aborted in the first weeks of pregnancy. It is well known that male embryos have a much better chance of implantation in the uterus of the mother than female embryos, but that they simultaneously have a much greater chance that they will be aborted in the first weeks of pregnancy. Of a ratio of the sexes of 1.64:1 in favour of boys in the 5–7th week of pregnancy, the secondary sex index usually decreases by the time of parturition to the usual value of 1.06:1, corresponding to 106 newborn boys to 100 newborn girls. The immune system of the mother plays an important role in elimination of male embryos as it recognizes antigens specific for male cells, H–Y antigens. It is known that toxoplasma has a substantial impact on immune processes occurring in the infected organism. Thus, it is possible that toxoplasma can affect the ratio of the sexes in favour of boys by suppressing the component of the immune system that is responsible for elimination of male embryos. In conclusion, two questions to make you think: Older parasitologists observed that, in a population in which about 30% of the individuals are infected by toxoplasma, more than 80% of children with Down’s syndrome are born to mothers infected by latent toxoplasmosis. Modern parasitologists and physicians, of course, laughed at this – we obviously know that Down’s syndrome is not caused by a parasitic protozoa but by the fact that two copies of chromosome number 21 accidentally entered the egg during meiosis and the individual was created by the fertilization of this egg by normal sperm so that the individual has three copies of this chromosome in their cells instead of two. The first question – how could toxoplasma lead to increased frequency of children with Down’s syndrome in infected mothers, without having to attack the future sex cells and play around with their chromosomes during meiosis? Second question, far more difficult, to which I also do not know the answer – should parents who are taking care of a beloved child with Down’s syndrome curse toxoplasma or thank it?
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The Green Beard Model
In this model, Dawkins shows that the alleles of genes are quite selfish; that each of them is interested only in the number of copies of itself that it can pass on to the next generation and not the number of copies of other genes in the genome, of which it is a part, that are passed on to the next generation. Let’s imagine Dawkins’ hypothetical green-beard allele, which leads to the formation of a green beard in its carriers and also leads them to assist other “green-beards”. It can be seen (and it’s very easy to demonstrate on a mathematical model) that such a green-beard allele has a much greater chance of spreading in evolution than an allele that would lead its carriers to help their blood relatives. The carriers of green-beard alleles will pass (and will help to pass) on to the next generation more copies of themselves than copies of other alleles. On the other hand, an allele that would lead its carriers to assist blood relatives will be worse off, even though it would objectively ensure that a greater percentage of all the alleles (of all the genes) of its carrier are passed on to the next generation. However, it would not ensure that carriers of itself would be amongst them more frequently than the carriers of alternative alleles occurring on the second copy of the same chromosome. The unrelenting laws of biological evolution thus mean that each allele will behave quite selfishly and will be completely indifferent to the fates of the other alleles on the same chromosome or in the same genome. The only thing that it will count will be the number of copies of itself that it passes on to the next generation.
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The Mandelbrot set
This is a set of elements that belongs to the plane of complex numbers (in the figure, the abscissa corresponds to the real part and the ordinate corresponds to the imaginary part of a particular complex number c) that, even after repeated substitution into the (recurrent) equation
zn+1 = zn2 + c (where z0 = 0),
does not exceed a value of 2. Some points in the plane of complex numbers exceed a value of 2 in the very first substitution into the equation, while this occurs for others only when the given procedure, i.e. addition to its square and substitution of the result into the right-hand side of the equation, is repeated many times. The number of these repetitions (iterations) required to exclude that a particular point belongs to the Mandelbrot set is depicted by the degree of grey in the figure. (A much nicer picture is created when the numbers of repetitions are depicted in various colours.)
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The Prisoner’s Dilemma and the Tit for Tat strategy
The Prisoner’s Dilemma game is a favorite subject of analysis for theoretical biologists. This game has many versions, one of which can, for example, be described as follows: Two offenders were caught after they committed a serious crime. There is no direct evidence against them so that, if they cooperate, i.e. deny their guilt, no one can prove their main crime and they will be sentenced only for secondary crimes, such as having possession of a stolen object, with a relatively milder punishment, for example, 3 years in prison. The prisoners are closed in their separate cells and each receives the following offer. If he confesses first and designates his accomplice as the principal guilty party, then he will receive only a mild punishment, for example, one year in prison. However, if he denies his guilt, while the other prisoner who received the same offer, confesses first, then he will receive a sentence of many years. However, if they both betray their accomplices, each will receive a sentence of 5 years in prison. In theoretical studies, the game is played for points rather than years in prison. Usually a game is analyzed in which the reward is 3 points for mutual cooperation, 1 point for mutual betrayal and 5 points for the betrayer and 0 points for the betrayed in one-sided betrayal. Mathematical analysis of the problem demonstrates that, under the given conditions, it is preferable for either of the prisoners to immediately betray his accomplice and not expose himself to the risk of being the second to opt for this approach. The course of a large portion of actual interrogation processes indicates that most offenders do not need to be conversant with the mathematical apparatus of game theory in order to find the only right strategy. Situations that are more or less similar to the prisoner’s dilemma are, of course, encountered in nature. An individual sometimes finds himself in a situation where he must choose between betrayal, which can bring great profit or only a small loss, and cooperation, which can bring average profit if the partner also cooperates, but a major loss if the partner betrays him. Under conditions where the two partners will not meet again in the future, or where organisms are involved that cannot recognize or remember their former opponents, both individuals will almost certainly make a choice in accordance with the theory of the “always betray” strategy. A different situation occurs if two individuals play the Prisoner’s Dilemma game repeatedly and are capable of remembering the course of the last game. Then the Tit for Tat strategy turns out to be very advantageous. This consists in cooperation in the first game and then, in future games, always repeating the strategy of the other player in the previous game. In nature (and human society), the same opponents frequently meet repeatedly. Consequently, a strategy similar to the Tit for Tat strategy is often employed.
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The theory of neutral evolution
This theory is concerned with study of the evolution of selectively neutral traits, i.e., for example, a large part of changes in the DNA sequence. As, in some cases, up to six various triplets of nucleotides code the same amino acid, a change in the DNA need not have any effect on the amino acid sequence of the protein that is coded by this DNA. Thus, mutations that do not affect the sequence of proteins can be invisible for selection and thus their spreading and accumulation in the genome must occur through some other process than selection. Traditionally, primarily genetic drift is considered; however newer discussions consider genetic hitchhiking (which may be more significant). Neutral evolution may be responsible for the evolution of a greater number of traits than selection alone (however, this is not entirely certain6) and can thus substantially contribute to the diversification of species and possibly also to speciation (the splitting off of new species). However, the most interesting class of traits – adaptive traits – cannot be created by the processes of neutral evolution.
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Variability within a population
This is more or less the same as polymorphism in a population or, simply, heterogeneity. The members of a single species (to be exact, it should be added – of the same sex and age) differ from one another in external appearance and internal traits. If we simplify this a bit, we can state that the different effects of the environment, for example, different nutrition, are responsible for some differences (and these differences are not transferred to offspring), while other differences lie in the genotypes of the individual organisms (and these differences are inherited from their parents by descendants).
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Why aren’t there two-headed mutants running around after Chernobyl?
Because the relevant embryos with developmental defects were not embedded in the uterus and were aborted. This process has been studied in detail in rodents and in cattle exposed to high radiation levels in the vicinity of the Chernobyl nuclear power plant. These animals did not produce more deformed young, but their fertility was substantially reduced. And that is not all. It was found that, under the new conditions of elevated radiation, heterozygote individuals very frequently produced, with different probability, descendants with one or the other allele – i.e. exactly that phenomenon that we discussed in connection with the S allele. By the way, infant mortality increased substantially in Eastern Europe after the Chernobyl nuclear power plant exploded. It can be expected that a similar change (in this case, on the other hand, a decrease) could be found in the fertility of the inhabitants of Europe (e.g. in the average period of time that a pair waited for a child). It is quite probable that, in addition to reducing the population growth, the explosion of the Chernobyl power plant was also manifested in the composition of the gene pool of the European population (because of the above-mentioned changes in the probability of transmission of the individual alleles to the next generation).
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Why do elephants change faster than mice?
Compared to small rodents, elephants have a much longer generation period. Nonetheless, palaeontological data indicate that they changed much faster during evolution than, for example, mice. The theory of genetic draft could provide a possible explanation for this. Because of their longer generation period, elephants live in a sort of rapidly changing world. During one generation period of mice (two months) the environment (for example, also the climate) doesn’t change much (this does not apply to cyclic changes related, e.g., to the seasons of the year, but rather to long-term changes to which species react in evolution); however, substantial changes can occur during the generation period of an elephant. Consequently, elephants must adjust to new conditions in each generation and consequently new suitable alleles are quite frequently fixed in their populations. And neutral and only slightly harmful mutations hitchhike along with them; these need not affect the appearance of the elephant but can increase the probability that they will evolve into a new species, see the hypothesis of the formation of reproduction barriers as a consequence of accumulation of incompatible mutations. Other explanations are also possible. For example, large animals usually form small populations; accident plays a more important role (compared to selection) in small populations, so that slightly harmful changes can accumulate more easily and thus faster in these populations. Both these phenomena are employed to explain the paradox of the molecular clock. Although most mutations are formed in copying DNA and thus in cell division during the formation of sex cells, the speed of the protein molecular clock, i.e. the speed of accumulation of mutations in proteins, does not depend on the generation period of the studied organisms. This is a result of the fact that, although fewer (slightly harmful) mutations are formed each year in elephants than in mice, a greater percent of them are fixed in elephants. In accordance with these hypotheses, synonymous mutations behave differently and their accumulation is not proportional to time measured in years but to time measured in generation periods.
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In many animals and some plants, the sex of an individual is determined at the time of merging of the male and female sex cells by the presence of sex chromosomes. Mammals are an example of organisms in which the male carries two kinds of sex chromosomes, the X and the Y chromosome, while the female has both sex chromosomes the same, i.e. has two X chromosomes. During meiosis, the two sex chromosomes form a pair and then separate (similar to the other pairs of homologous chromosomes), each to its newly forming sex cell. Thus, two types of gametes are formed in males, one with an X sex chromosome and the other with a Y sex chromosome. Females form only one type of gamete – all with an X chromosome. If, during fertilization, a male gamete bearing an X chromosome merges with a female gamete bearing an X chromosome, then a female embryo is formed. However, if a male gamete bearing a Y chromosome merges with a female gamete bearing an X chromosome, then a male embryo, XY, is formed. The Y chromosome carries genes that are necessary for the formation of male sex organs and the products of these male sex organs subsequently affect the entire development of the embryo in a way such that a male is formed.
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