Genetics PDF

Genetics A basic principle of modern evolutionary theory is that organisms attain their diversity through hereditary modifications of pre-existing similar ancestors. All known animals are related by descent from common ancestors. Hereditary establishes the continuity of life, although offspring usua...

Genetics A basic principle of modern evolutionary theory is that organisms attain their diversity through hereditary modifications of pre-existing similar ancestors. All known animals are related by descent from common ancestors. Hereditary establishes the continuity of life, although offspring usually vary in subtle ways from their parents. Some characteristics show resemblances to one or other parent, others are a blend of the two. What is actually inherited by an offspring are 'genes' (the genotype) which, under environmental factors, guide the physical characteristics, which are seen (the phenotype). The gene is the unit of inheritance, the basis for every characteristic that appears in an organism. The study of what genes are and how they work is called genetics. It is a science that deals with the underlying causes of resemblance and variation between individuals, populations and species. Genetics is one of the most important and unifying concepts in biology. It has shown that all living forms use the same information storage, transfer and translation system, and it provides an explanation for both the stability of all life and its descent from a common ancestral from. Some of the terms used in genetics can seem a little complex. However, if you work your way through slowly the connections will become clear. It is not necessary to fully understand all of the genetic theory, but the basic principles are very important. Mendel and inheritance Mendelian inheritance is a set of primary tenets relating to the transmission of characteristics from parent organisms to their offspring. They were derived from the work of the Austrian Monk, Gregor Mendel, and published in 1865 and 1866 but were 're-discovered' in 1900. When his ideas were integrated with the chromosome theory of inheritance, by Thomas Hunt Morgan, in 1915, they became the core of classical genetics. Mendel's now classic observations were based on garden peas, because pure strains (offspring always identical to parent plants) had been produced over a long period of time by careful selection in the Abbey gardens. He chose to use single characteristics (traits), which displayed sharp contrasts between different conditions - e.g. short or tall plants, yellow or green peas, smooth or wrinkled peas. He crossed one plant with one characteristic (e.g. green peas) with the other (yellow peas) by artificial fertilisation. When the cross-fertilised plant bore seeds he noted the characteristics of the hybrids grown from these seeds (know as the F1 generation). The 're-discovery' made Mendelism an important but controversial theory. Its most vigorous promoter in Europe was William Bateson, who coined the term 'genetics', 'gene', and 'allele' to describe many of its tenets. The model of heredity was highly contested by other biologists, because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observed in the natural world - e.g. people are not only short or tall, but may be almost a continuous scale of height. Many biologists dismissed the theory, because they were not sure it would apply to all species, as there seemed to be very few 'true Mendelian characters' in nature. However, later work by biologists and statisticians showed that if multiple Mendelian factors were involved for individual traits, they could produce the diverse amount of results observed in nature. The Law of Segregation, also known as Mendel\'s First Law, states that, 'in the formation of gametes, paired factors specifying different phenotypes (visible traits) segregate independently from each other'. (See section on meiosis later in the module). There are four underpinning facts, which support this theory. 1. Alternative versions of genes account for variations in inherited characteristics. This is the concept of alleles. Alleles are different versions of a gene that impart the same characteristic. For example, each human has a gene that controls eye colour, but there are variations among these genes in accordance with the specific colour for which the gene 'codes', e.g. blue, brown, green, etc. The locus of a gene is the area of a chromosome where a particular gene is found (where on a chromosome the gene is), e.g. at the locus of the agouti (tabby) gene in the cat, either the agouti (A) or non-agouti (a) allele can be found. 2. For each characteristic, an organism (if sexual reproduction occurs) inherits two alleles, one from each parent. This means that when somatic (non-gamete) cells are produced (they have pairs of chromosomes), one allele comes from the mother and one from the father. These alleles may be identical (true-breeding organisms or homozygous), or different (hybrids or heterozygous). The allele of a gene represents the different forms that genes can take. 3. Alleles of a gene exhibit dominance. If the two alleles differ, then one, the allele that encodes the dominant trait, is fully expressed in the organism\'s appearance; the other, the allele encoding the recessive trait, has no noticeable effect on the organism\'s appearance. In other words, only the dominant trait is seen in the phenotype of the organism. This allows recessive traits to be passed on to offspring even if they are not expressed. An allele is said to be dominant when its expression prevails over any other copy of the gene in the cell. For example, agouti (tabby) is a dominant allele in the cat, so any cat having at least one agouti allele will have a visibly tabby coat. When expressing genetic information, a particular shorthand is used; all dominant alleles are referred to with a capital letter, e.g. A, B, C. Recessive alleles need to be present on both chromosomes to be expressed, i.e. no dominant allele can be present for the recessive characteristic to be 'seen'. If a recessive allele is paired with a dominant allele, it will not be 'visible' in the organism. For example, a cat that has inherited the agouti gene from both parents will be AA and tabby in appearance (genotypically and phenotypically tabby). The cat that inherits one agouti and one non-agouti gene will be Aa, and will appear to be tabby in appearance (heterozygous genotype, tabby phenotype). Only if the cat inherits non-agouti from both parents, will the cat have a solid coloured coat aa (homozygous recessive genetically, phenotype non tabby). 4. The two alleles for each characteristic segregate during gamete production. This means that each gamete will contain only one allele for each gene. This allows the maternal and paternal alleles to be combined in the offspring, ensuring variation. A tool often used by animal breeders is the Punnet square. It can be used to determine the potential different genotypes of offspring from a specific mating. The alleles contained in the gametes from one parent are placed along the top, those from the other along the side. Since each gamete contains only one of a pair, only a single letter for each gene is present. For example, continuing with the example of agouti and non-agouti (tabby and self pattern), if both parents are heterozygous for tabby, the following Punnet square would result. Example 1: both parents heterozygous 50% eggs carrying A 50% sperm carrying A 25% AA homo tabby 50% eggs carrying a 50% sperm carrying a 25% Aa hetero tabby 25% Aa hetero tabby 25% aa homo self Each sperm cell carries either A (agouti) or a (non-agouti), each egg cell will similarly carry either an A or a. The four inner sections represent the possible genotypes of the offspring. A quarter will be AA homozygous tabby, a quarter homozygous self aa, and 50% will be heterozygous tabby Aa. As A is dominant to a, all the kittens will be phenotypically tabby. Mathematically, the visible traits seen in kittens will be three tabbies, and one self. NB. However, as each potential kitten is formed of a random pairing of gametes, and the number of kittens present in a litter is variable, the actual ratio found in a particular litter may not be as above, it is also possible that all the kittens will be tabby, or 50% non-tabby. This type of square is also useful if the parents genotype is unknown, it can be useful to determine whether a parent is homozygous or heterozygous for a characteristic, This is known as a test mating - i.e. mating a heterozygous 'suspect' parent (is it AA or aa?) to a homozygous recessive cat e.g. aa. Then, if any of the offspring were non-tabby, the suspect parent must be heterozygous. Example 2: determining parent genotype Homozygous recessive a Tabby A or a Aa or aa Homozygous recessive a Aa or aa Tabby A or a Aa or aa Aa or aa Any aa offspring means the parent is a heterozygote for the gene in question. Again, such a test mating would have to be repeated several times to determine if the parent was a heterozygote. For example, you could flip a coin five times and gets heads every time, but assuming the coin had two heads, (and no tails) there would not be a valid conclusion unless a great many more 'flips' had been carried out. Even though statistics say heads and tails should occur in equal numbers, this does not always occur in a limited sample. Mendel's Second Law: The Law of Independent Assortment, states that the inheritance pattern of one trait will not affect the inheritance pattern of another. In terms of gene theory, this means that genes located on different pairs of homologous chromosomes assort independently during meiosis. While his experiments with mixing one trait always resulted in a 3:1 ratio (example 1) between dominant and recessive phenotypes, his experiments with mixing two traits (dihybrid cross) showed 9:3:3:1 ratios. Example 2 shows that each of the two genes are independently inherited with a 3:1 ratio. Mendel concluded that different traits are inherited independently of each other. Example 2: dihybrid cross In the pea plant, two characteristics for the peas, shape and colour, can be used to as an example of a dihybrid cross in a Punnett square. R is the dominant gene for roundness of shape in pea seeds, with r denoting the recessive wrinkled shape. Y = dominant yellow pea, and y = recessive green coloured pea. The gametes for the Punnett square from the parent plants are, therefore, RY (round and yellow), Ry (Round and green), rY, (wrinkled and yellow) and ry (wrinkled and green). RY Ry rY R Y RRYY RRYy ry RrYY R y RRYy RRyy RrYy RrYy r Y RrYY RrYy Rryy rrYY r y RrYy Rryy rrYy rrYy rryy The result in this cross is a 9:3:3:1 phenotypic ratio, as shown by the colours, where yellow represents a round yellow (both dominant genes) phenotype, green representing a round green phenotype, red representing a wrinkled yellow phenotype, and blue representing a wrinkled green phenotype (both recessive genes). The reason for this is that during meiosis (gamete producing cell division), the member of any pair of homologous chromosomes (received by a particular gamete) is independent of which member of any other pair of chromosomes it receives. Multiple alleles Whereas an individual can have no more than two alleles at a particular locus (one on each chromosome of a pair), many more dissimilar alleles can exist in a population. Multiple alleles arise through mutations at the same gene locus over time. Any gene may mutate, and can give rise to slightly different alleles at the same locus, however unless the more recessive forms occur in a homozygous animal, they may never be actually seen phenotypically. For example, unless two albino rabbits (or those carrying the recessive albino gene) mate, no albinos will be seen, even though the gene will be passed through successive generations. Gene interaction The types of crosses presented above are simple in that the trait variation results from the action of a single gene. In reality, many traits are the result of interaction between two or more genes, and many different genes affect individual characteristics (polygenetic inheritance). In addition, many genes have more than a single effect on a phenotype, this is known as pleiotrophy, e.g. a gene which influences eye colour, may also mask or prevent the expression of an allele on another locus acting on the same trait. This is known as epistasis. Another form of interaction occurs when several different alleles produce a cumulative effect on the same characteristic. The number of chromosomes in any organism is relatively small, compared with the huge number of traits, so therefore, each chromosome contains many genes. All genes on the same chromosome are said to be linked. Crossing over Linkage is, however, seldom complete. When performing crosses with animals such as Drosophila (fruit fly), linkage traits separate in a small percentage of offspring. These separations of alleles on the same chromosomes are due to crossing over. During the first phase of gamete producing cell division, (meiosis) paired homologous chromosomes break and exchange equivalent portions, thus genes can 'cross over' from one chromosome to its homologous partner. Meiosis and gamete production Meiosis is the process by which one diploid (each chromosome has an alternate within the cell) eukaryotic cell divides to generate four haploid (has non-paired chromosomes) cells called gametes. The genetic material is replicated once and separated twice, producing four haploid cells each containing half of the original cell\'s chromosomes. These resultant haploid cells can fuse with other haploid cells of the opposite sex during fertilisation to create a new diploid cell or zygote. The word 'meiosis' comes from the Greek meioun, meaning 'to make smaller', as it results in a reduction in chromosome number in the gamete cell. Meiosis is essential for sexual reproduction and occurs in all eukaryotes that reproduce sexually. Without the halving of the number of chromosomes, fertilisation would result in zygotes that have twice the number of chromosomes than the zygotes of the previous generation. As chromosomes of each parent undergo genetic recombination during meiosis, each gamete, and thus each zygote, will be unique genetically. Thus meiosis and sexual reproduction produce genetic variations. Meiosis uses many of the same biochemical and physical mechanisms employed during mitosis to accomplish the redistribution of chromosomes. There are several features unique to meiosis, most importantly the pairing and genetic recombination between homologous chromosomes. Recombination and independent assortment allow for a greater diversity of genotypes in the population, allowing a species to maintain stability and adapt to environmental changes. Evolution Pre-Darwin theory Before the 18th century, speculation on the origin of species rested on creationism, where the world has remained constant since the Earth was created by divine being (s) depending on the religion. Early Greek philosophers (Xenophanes, Empedocles and Aristotle) developed a theory that species change, as they recognised fossils as evidence that some organisms existed in the past that were not present in their time. However, they assumed these organisms died from natural disasters. Lamarckism French biologist Jean Baptiste de Lamark proposed the first complete explanation of evolution (called the inheritance of acquired characteristics) in 1809, the year Charles Darwin was born. Lamark proposed his mechanism to account for extinctions over time, using fossil evidence that certain animals no longer existed. He proposed that organisms striving to meet the demands of their environment acquire adaptations, which they then pass on to their offspring, e.g. an ancestral giraffe had to stretch neck and legs to reach high food items as lower down food was unavailable, resulting in longer limbs/necks, which are then inherited by their young. This transformational concept of evolution proposed that individual organisms transform their characteristics to produce overall species changes (evolution). Darwin's theory is a contrasting variational theory, caused by distribution of genetic variation in populations and differential survival/reproduction in individuals with different hereditary traits. Uniformitarianism The geologist Charles Lyell proposed (in 1830) that the laws of chemistry and physics remain the same throughout the history of the Earth, and that past geological events occurred by natural processes acting over long periods, explaining the formation of fossil bearing rocks. Lyell also stressed the gradual nature of geological changes over very long periods, an idea which greatly influenced Darwin. Charles Darwin Darwin developed his interest in natural history while studying first medicine, then theology. His five-year voyage on the Beagle established him as a geologist whose observations and theories supported Lyell\'s uniformitarian theories. Puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin investigated the transmutation of species (the gradual change of one species into another) and conceived his theory of natural selection in 1838. His 1859 book, On the Origin of Species, established evolution by common descent as the dominant scientific explanation of diversification in nature. Darwinian evolutionary theory: the evidence Perpetual change The main underpinning idea behind Darwinian evolution is that the living world is neither constant, nor in a state of perpetual cycling, but is nevertheless constantly changing. Evidence for this perpetual change is seen directly in the fossil record. A fossil is a remnant of past life uncovered from the crust of the earth. They come in various forms from complete remains (e.g. mammoths, or insects in amber) to actual hard parts (teeth and bones), petrified skeletal parts that are infiltrated with silica or other minerals (ostraderms and molluscs) and finally other fossils including, moulds, casts, impressions and coprolites (fossil excrement). Because many organisms left no fossils, a complete record of the past is probably never going to be available. However, discovery of new fossils and reinterpretation of previous discoveries expand our knowledge of how animal life has changed over time. Fossil insect in amber Carcharodontosarus Coprolite and Megaladon teeth The fossil record is, however, biased because preservation is selective with vertebrate skeletal parts and invertebrate shells/other hard body parts leaving superior records. Soft-bodied animals such as worms and jellyfish are seldom fossilised. Fossils are deposited in stratified layers, with new deposits on top of older ones, thus a sequence occurs with the ages of fossils being directly related to their depth within stratified layers, and different layers are characterised by the fossils they contain. Unfortunately, layers are rarely undisturbed, geological processes such as erosion or human intervention result in incomplete disturbed evidence, which is difficult to interpret. Evolutionary trends The fossil record allows evolutionary changes to be seen over very long periods of time. Species arise and become extinct repeatedly throughout the history of the Earth. Animal species typically survive approximately one million to ten million years, although their duration is highly variable. Trends (directional changes in the characteristic features or patterns of diversity in a group of organisms) can often be seen in particular groups of species. One of the better-documented cases is the fossil evidence of the evolution of horses from the Eocene era to the present. Other species replaced many different species throughout time (only the main groups are depicted below). The three characteristics, which show the clearest trends in horse evolution are body size, foot structure and tooth structure. Compared to modern horses, extinct genera were small, with teeth having a small grinding surface, and feet with a larger number of toes (four). Throughout the Oligocene, Miocene, Pliocene and Pleistocene eras, there were continuing patterns of new genera arising as the older ones became extinct. In each case, a net increase in body size, grinding surfaces of teeth and a reduction in the number of toes occurred. As the number of toes decreased, the central digit became increasingly prominent, until only this digit remained. The fossil record shows a net change not only in the characteristics of horses, but also variation in the numbers of different horse genera and numbers of species that have existed through time. The sole survivor of this largely extinct group is the genus equus. Common ancestry Darwin proposed that all living things have descended from a common ancestral organism. Life's history is often depicted as a branching tree, called a phylogeny. Pre-Darwinian evolutionists, including Lamark, advocated multiple independent origins to life, each of which gave rise to lineages, which changed throughout time without extensive branching. The classification and phylogeny of animal species is examined in the next module. Homology Darwin recognised the major source of evidence for common ancestry was the idea of homology. Anatomical structures that perform the same function in different biological species and evolved from the same structure in an ancestral species are called homologous. A classic example of homology is the limb skeleton of vertebrates. Bones of vertebrate limbs maintain characteristic structures and patterns of connection despite diverse modification for different functions. The pentadactyl limb Ontogeny, phylogeny and recapitulation Ontogeny is the history of the development of an organism throughout its entire life. Early developmental land embryological features contribute greatly to our knowledge of homology and common decent. The German zoologist Ernst Haeckel (a contemporary of Darwin) believed that each successive stage in the development of an individual represented one of the adult forms that appeared in its evolutionary history. The human embryo, having gill depressions, was believed to resemble the adult appearance of a fish-like ancestor. Thus, ontogeny (individual development) recapitulates (repeats) phylogeny (evolutionary decent). This is also known as recapitulation or the biogenetic law, although later theorists proposed that early developmental features were simply more widely shared amongst different animal groups than latter ones. The adult stages of animals with relatively simple ontogenies simply resemble the early stages in the development of more complex organisms. Ontogeny in chordates Multiplication of species Multiplication of species over time is the logical result of Darwin's theory of common descent. A branch point on the evolutionary tree occurs when an ancestral species splits into two different ones. Members of a species are descended from a common ancestor, are reproductively compatible, and have consistency of genotype/phenotype. Speciation is the process by which a single population of organisms becomes reproductively unique and a separate species. Biological barriers, which prevent different species reproducing, are called reproductive barriers. Speciation is thought to occur in two ways: Speciation that results from the evolution of reproductive barriers between populations that are geographically separated is called allopatric speciation. It can begin in two ways, firstly by vicariant speciation, where geological changes fragment a species habitat. In this instance, say a flood or fault divides a habitat, more than one species is usually affected at a time. Alternatively, allopathic speciation can be due to a founder event, when a small number of individuals disperse to a distant area where no members of their species currently exist. This often results in dramatic phenotypic changes in the population, as the gene pool is initially so small. Biologists often distinguish between reproductive barriers that impair fertilisation (pre-mating barriers) and those, which impair growth and development, survival or reproduction of hybrid individuals (post mating barriers). Pre-mating barriers may be anatomical, divergent populations may have incompatible genitalia, may not recognise each other as possible sexual partners, or behavioural, not completing the mating ritual successfully. Species, which appear phenotypically identical, are known as sibling species, but do not reproduce together due to variations in seasonal breeding, auditory, chemical, or behavioural signal required for breeding to occur. After a founder event has occurred, it is likely adaptive radiation will take place. In volcanic islands such as the Galapagos, the ancestral finches, which were probably blown to the islands in very small numbers, multiplied and specialised into at least 14 different species, a process known as adaptive radiation. Non-allopathric speciation This occurred in habitats such as the Great Rift Lakes of Africa, (Lake Malawi, Lake Tanganyika and Lake Victoria) where many closely related species of chilid fish exist in the same location. To explain speciation in cases such as this, sympatric speciation has been proposed. According to this hypothesis, different individuals within a species became specialised for occupying different niches within the habitat. By seeking out and using very specific habitats in a single geographical area, different populations achieve sufficient physical and adaptive separation to evolve reproductive barriers. For example, different African chilids species have different feeding specialisations and parasitic insects have different host animals. Natural selection Natural selection is the primary principle of Darwin's theory of evolution. It gives a natural explanation for the origins of adaptation, including all developmental, behavioural, anatomical and physiological attributes that enhance an organism's ability to use environmental resources to survive and reproduce. Darwin developed his theory of natural selection as a series of five observations, and three inferences drawn from them: Observation 1 Organisms have great potential fertility. Observation 2 Natural populations normally remain constant in size except for minor fluctuations (no natural population expands at the rate which is suggested by the possible number of offspring). Observation 3 Natural resources are limited. Inference 1 A continuing struggle for existence exists amongst members of a population. Observation 4 Populations show variation amongst individuals. Observation 5 Some variation is heritable. Inference 2 traits. Varying organisms show differential survival and reproduction favouring advantageous Inference 3 Over many generations, differential survival and reproduction generate new adaptations and therefore eventually new species. Natural selection can be seen as a two-step process with a random component, production of variation amongst organisms, which may produce disadvantageous characteristics as well as favourable ones, and a non-random component (survival due to the differential traits). Microevolution This is the study of genetic change within natural populations. The observation of different allelic forms of a gene in a population is called polymorphism and all alleles of all genes with a population are known as the gene pool of that population. Genetic equilibrium refers to the ratio of allelic frequency and genotype ration within a population, which remains stable over time. Genetic equilibrium can be disturbed in a number of ways; by random genetic drift, by non-random mating, recurring mutation, migration and natural selection (and interaction amongst these factors) leading to the eventual evolution of one species into another. Genetic drift occurs particularly in small populations where the population does not have enough diversity; certain alleles become concentrated, due to the small number of breeding animals. In species such as the cheetah, the high degree of genetic drift means the species may become extinct due to its lack of genetic diversity; a single disease could wipe out the population. Non-random mating, e.g. if albino individuals mate with others with their colouring within a population, the number of albino individuals will increase out of proportion to the expected ratio given the frequency of a recessive allele in the population as a whole. This process is also known as inbreeding and together with genetic drift are processes, which affect small populations. These effects are decreased if a population engages in migrations, with the result that different groups meet and may engage in intergroup reproduction, increasing diversity. Macroevolution Macroevolution describes large-scale events in organic evolution. Three tiers of effects have been described; the first constitutes the processes of population genetic processes (micro-evolution) occurring over tens to thousands of years. The second tier covers millions of years, and covers processes such as speciation and extinctions, the third tier covers hundreds of millions of years and is characterised by periods of mass extinctions. The fossil record shows that mass extinction occurs at approximate intervals of 26 million years, and is currently thought to be due to asteroids impacts. The most dramatic occurring in the Permian era, 225 million years ago, when 90% of marine invertebrate species became extinct within a few million years. The Cretaceous extinction, 65 million years ago, marked the end of the period of dinosaur domination. The proliferation of mammalian species after the dinosaurs' extinction has been referred to as catastrophic species selection, as the mammals evolved to utilise resources, previously exploited by dinosaur species. The reproductive process Two modes of reproduction are recognised, asexual and sexual. In asexual reproduction, there is a single parent and there are no specialised reproductive organs, each individual is capable of producing offspring genetically identical to itself when adult. Sexual reproduction usually involves two parents who produce specialist gamete cells, which fuse (fertilisation) to produce a zygote. The zygote contains genetic material from both parents, and is a genetically unique individual. Asexual reproduction Asexual reproduction occurs in bacteria and unicellular eukaryotes and in many invertebrate phyla, e.g. cnidarians, bryozoans, annelids, echinoderms and hemichordates. Many of these animals can also reproduce sexually. There are several forms of asexual reproduction: Binary fission occurs in bacteria and protozoa. The body of the parent divides by mitosis into two equal parts, which then grow to the size of the 'parent' cell before dividing again. Binary fission may be longitudinal (flagellated protozoa) or transverse (ciliated protozoa). Multiple fission involves the nucleus, which divides many times within a parent cell before the cytoplasm, multiple 'daughter' cells are formed at the same time, e.g. 'spore' formation in parasitic protests such as malarial parasites. Budding is the unequal division of an organism, a new individual arises as an outgrowth from the parent, before detaching itself, common in cnidarians (coral animals). Gemmulation occurs in freshwater sponges and is the formation of a new individual from an aggregation of cells surrounded by a resistant capsule (gemmule). In this form, they survive periods of adversity such as extreme cold or drought. Fragmentation occurs when a multicultural animal breaks into two or more parts, with each part capable of becoming a complete individual. Parthenogenesis occurs when an unfertilised egg develops into a new individual. Parthenogenesis occurs naturally in invertebrates (e.g. water fleas, aphids, some bees and parasitic wasps), and vertebrates (e.g. some reptiles, amphibians, fish, and, very rarely, birds). It is an abbreviation of the usual steps needed to reproduce sexually, and, as it involves meiosis, is sometimes categorised as an aberrant form of sexual reproduction. It may have evolved to solve the problem of bringing males and females together for mating at the right time, or to produce specific characteristics in the 'clone' offspring, e.g. male bees (haploid) result from unfertilised eggs. Sexual reproduction Bisexual reproduction is the production of offspring formed by the union of gametes from two genetically different parents, who, in the great majority of cases, are of two different sexes, male and female. Each sex has its own reproductive system and produces only one kind of gamete, spermatozoa or ova. Nearly all vertebrates and many invertebrates are dioeciously species (having two sexes), although some are monoecious (hermaphrodites). Distinctions between the sexes are based not on size or appearance but on the size and motility of the gamete they produce. The ovum (egg) is produced by the female, and is comparatively large due to the stored yolk to sustain early development. The spermatozoon (sperm) is relatively small, motile and produced in far greater numbers; its single purpose is fertilising the egg. The other distinctive feature of sexual reproduction is meiosis, as discussed above. Many unicellular organisms reproduce both sexually and asexually. In some cases, two organisms merely join together to exchange nuclear material (conjugation) so reproduce sexually without the presence of distinct sexes. Organs that produce gametes are known as primary sexual organs (gonads). The testis is the organ producing sperm, and eggs are formed in an ovary. Accessory sexual organs are found in most complex organisms, including in males, the penis and in females, the uterus, uterine tubes and the vagina. Some organisms have both male and female gonads. Groups that adopt a sessile (stationary), burrowing or end parasitic lifestyle (e.g. flatworms, annelids, barnacles and a few vertebrate fish species) operate this system. A minority of these species self fertilise, but most exchange gametes with a sexual partner. An advantage is that a hermaphrodite species (with all individual bearing young rather than only the females) could theoretically produce twice as many offspring as a similar dioeciously species. Some fish are sequential hermaphrodites, in that, at a certain age they undergo a sex change from an active reproducing member of one sex to a member of the other (female to male or male to female depending on species). Reproductive patterns The majority of invertebrates and many vertebrates are 'oviparous'. That is, they lay eggs in the environment in which they will develop. Fertilisation can either be internal (eggs are fertilised inside the body of the female), or externally (eggs are fertilised after the eggs have left the females body). Many oviparous species simply abandon their eggs, whilst others display extreme care, and provide suitable resources for their young as they develop. Ovoviviparous species retain fertilised eggs within the body cavity (usually oviduct) where they receive nourishment from the egg, for a period of time, e.g. some annelids, brachiopods, insects, gastropod molluscs and some fish and reptiles. Viviparous animals nurture embryos within oviducts or uteri, with the embryos deriving nourishment from the mother. Viviparity is confined mostly to mammals and elasmobranches fish, although viviparous invertebrates, e.g. scorpions, amphibians and reptiles, occur. Development of embryos within the mother's body is an advantage, as it offers protection to the young when vulnerable, however the number of young produced is severely reduced compared to oviparous species. Invertebrate reproductive systems Invertebrates that use internal fertilisation possess reproductive systems as complex as many vertebrates. In contrast, others simply release gametes into water and their reproductive systems are little more than centres for gametogensis. For example, polycheate annelids produce gametes by a proliferation of cell lining the body cavity, which are released through coelmic or nephritic ducts or, in some cases, by rupture of the body wall. The female insect reproductive system is complex, consisting of a pair of ovaries, which are subdivided into smaller units called ovarioles, where the eggs are produced. As the oocytes grow, they are pushed downwards by the continual cell division in the germarium. The oocytes form chains, with the youngest/smallest cells at the top and mature/large cells at the bottom. When mature, eggs leave the ovary via the lateral oviduct and continue through the common oviduct, which opens into a genital chamber (called the bursa copulatrix). This is where the male deposits his spermatophore during copulation. The female uses peristaltic contractions to move the spermatophore into the spermatheca, where it is stored until it is needed. The spermathecal gland produces nutrients in order to keep the sperm alive in the spermatheca, where sperm can survive for weeks, months or even years. When the egg enters the genital chamber, it passes across the spermatheca and stimulates the release of sperm cells onto the egg surface. Oviposition (egg laying) soon takes place following fertilisation. In the male, sperm from the testes pass through sperm ducts to seminal vesicles where they are stored. They proceed through a single ejaculatory duct to a penis (aedeagus). Vertebrate systems In vertebrates the reproductive and excretory systems are jointly called an urogenital system, because of their close anatomical connection. In male fish, the duct, which drains the kidney, also serves as a sperm duct (mesonephric/wolffian duct). In male reptiles, birds and mammals, where the kidney has an independent duct (ureter) the separate sperm duct (developed from the wolffian duct) is called a vas deferens. In all these forms, (except mammals) the ducts open into a cloaca, a common chamber into which intestinal, reproductive and excretory tracts empty. Almost all placental mammals have a separate opening for the intestinal systems and uro/reproductive system. The human reproductive system below is fairly typical of vertebrate reproductive systems, although a penis only occurs in some birds and all reptiles and mammals, other species mate cloaca to cloaca. Both testes and ovaries produce reproductive hormones. Timing of reproductive cycles Reproduction in most animals is seasonal to ensure an adequate food supply for the offspring is available. Reproduction timing is controlled by hormones, which are regulated by food intake, light levels, rainfall, temperature or by social cues. The hypothalamus of the brain is stimulated by these factors (according to species) and regulates the neurosecretory anterior pituitary gland, which in turn regulates the secretory activity of the gonads. The cyclic reproductive patterns of mammals are of two types, oestrous (most mammals) and menstrual (anthropoid apes, humans, monkeys and apes). In oestrous cycles, females are only receptive to males during short periods of oestrus (or heat). Menstruating animals may be receptive throughout the cycle. Another difference is that in a menstrual cycle the end of each cycle is characterised by a breakdown and shedding of the uterine lining if pregnancy is not established. In an oestrus animal, the uterus returns to its pre oestrous state with no shedding if not pregnant. Principles of development Fertilisation Before fertilisation can occur, it is necessary for the sperm and eggs to meet. In species that have internal fertilisation, this is less of a problem than in invertebrate species, which liberate gametes into water. In these species, (e.g. sea urchins) eggs release a chemo tactic molecule, which is species- specific, attracting only the sperm of its own species. Egg-recognition proteins on the head of the sperm bind to species- specific receptor proteins on the egg membrane making sure only the same species fertilisation occurs. These species- specific proteins are also found in vertebrate, (including mammalian) sperm and egg cells. At the point when a sperm contacts an egg membrane, immediate changes occur in the egg membrane, which prevents any other sperm fusing with the egg cell to prevent polyspermy. Fertilisation Once the sperm and egg membranes have fused, the sperm loses its flagellum, which disintegrates. The sperm pronucleus travels to the egg nucleus and fusion occurs. The resultant cell is now a diploid zygote. Fertilisation blocks the inhibitors, which stop the egg cell dividing and reduce metabolism, and the cell prepares for cleavage. Cleavage and early development During cleavage, the zygote undergoes rapid mitotic divisions with no significant growth, producing a cluster of cells that is the same size as the original zygote. The different cells derived from cleavage, up to the blastula stage, are called blastomeres. Depending mostly on the amount of yolk in the egg, the cleavage can be holoblastic (total) or meroblastic (partial). Holoblastic cleavage occurs in animals with little yolk in their eggs, e.g. many invertebrates and mammals. Meroblastic cleavage occurs in animals whose eggs have more yolk, i.e. birds and reptiles. Because cleavage is impeded in the vegetal pole, there is a very uneven distribution in the size of cells, being greater and bigger at the animal pole of the zygote. In holoblastic eggs, the first cleavage always occurs along the vegetal-animal axis of the egg, the second cleavage is perpendicular to the first. From here, the spatial arrangement of the blastomeres can follow various patterns, due to different planes of cleavage, in various organisms: Cleavage patterns followed by holoblastic and meroblastic eggs Holoblastic Radial (sea urchin, amphioxus) Bilateral (tunicates, amphibians) Spiral (annelids, molluscs) Rotational (mammals). Meroblastic Discoidal (fish, birds, reptiles Superficial (insects). Gastrulation After the cleavage has produced over 100 cells, the embryo is called a blastula. The blastula is usually a spherical layer of cells (the blastoderm) surrounding a fluid-filled or yolk-filled cavity (the blastocoel). Mammals at this stage form a structure called the blastocyst, characterised by an inner cell mass that is not present in the blastula. Gastrulation involves extensive cell movements, and, in most animals, gastrulation converts the spherical blastula into a more complex arrangement of three layers. The embryo during this process is called a gastrula. Germ layers formed at gastrulation differentiate into tissues and organs. The ectoderm gives rise to the skin and nervous system, the endoderm gives rise to the alimentary canal, pharynx, lungs and certain glands, the mesoderm differentiates into muscular, skeletal, circulatory, reproductive and excretory organ systems. Among the different animals, different combinations of the following processes occur to place the cells in the interior of the embryo: Epiboly - expansion of one cell sheet over other cells. Ingression - cells move with pseudopods. Invagination - forming the mouth, anus, and archenterons. Delamination - the external cells divide, leaving the daughter cells in the cavity. Polar proliferation Other major changes during gastrulation include cells starting to undergo differentiation processes. In most animals, a blastopore is formed at the point where cells enter the embryo. Development of systems and organs In animal development, organogenesis is the process by which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Internal organs initiate development in humans within the third to eighth weeks in utero. The germ layers in organogenesis differentiate by three processes: folds, splits and condensation. The notochord and neural tube are very early structures formed during organogensis. Vertebrate animals all begin to differentiate from the gastrula the same way, firstly developing a neural crest that differentiates into many structures including bones, muscles, and components of the peripheral nervous system. The coelom of the body forms from a split of the mesoderm along the somite axis. Differentiation of tissues in the early embryo generally consists of three general stages. Firstly, pattern formation (when the anterior, posterior, dorso-ventral and left/right orientation of the body is established), secondly, the determination of position within the body (when positions of major organ systems are established) and thirdly, the growth of limbs and organs appropriate for each position.