General Biology/Introduction to Evolution

Evolution is the process of change in all forms of life over generations. An organism inherits features called traits from its parents through genes. Changes called mutations in these genes can produce a new trait in the offspring of an organism. If a new trait makes these offspring better suited to their environment, they will be more successful at surviving and reproducing. This process is called natural selection, and it causes useful traits to become more common. Over many generations, a population can acquire so many new traits that it becomes a new species.

The understanding of evolutionary biology began with the 1859 publication of Charles Darwin's On the Origin of Species. In addition, Gregor Mendel's work with plants helped to explain the hereditary patterns of genetics. This led to an understanding of the mechanisms of inheritance. Further discoveries on how genes mutate, as well as advances in population genetics, explained more details of how evolution occurs. Scientists now have a good understanding of the origin of new species. This process is called speciation. They have observed the speciation process happening both in the laboratory and in the wild. This modern view of evolution is the principal theory that scientists use to understand life.

Darwin's idea: evolution by natural selection
Charles Darwin developed the idea that each species had developed from ancestors with similar features, and in 1838, he described how a process he called natural selection would make this happen. Darwin's idea of how evolution works relied on the following observations:
 * 1. If all the individuals of a species reproduced successfully, the population of that species would increase uncontrollably.
 * 2. Populations tend to remain about the same size from year to year.
 * 3. Environmental resources are limited.
 * 4. No two individuals in a given species are exactly alike.
 * 5. Much of this variation in a population can be passed on to offspring.

Darwin deduced that since organisms produce more offspring than their environment could possibly support, there must be a competitive struggle for survival - only a few individuals can survive out of each generation. Darwin realized that it was not chance alone that determined survival. Instead, survival depends on the traits of each individual and if these traits aid or hinder survival and reproduction. Well-adapted, or "fit", individuals are likely to leave more offspring than their less well-adapted competitors. Darwin realized that the unequal ability of individuals to survive and reproduce could cause gradual changes in the population. Traits that help an organism survive and reproduce would accumulate over generations. On the other hand, traits that hinder survival and reproduction would disappear. Darwin used the term "natural selection" to describe this process.

Observations of variations in animals and plants formed the basis of the theory of natural selection. For example, Darwin observed that orchids and insects have a close relationship that allows the pollination of the plants. He noted that orchids have a variety of structures that attract insects - so that pollen from the flowers gets stuck to the insects’ bodies. In this way, insects transport the pollen from a male to a female orchid. In spite of the elaborate appearance of orchids, these specialized parts are made from the same basic structures that make up other flowers. Darwin proposed that the orchid flowers did not represent the work of an ideal engineer, but were adapted from pre-existing parts, through natural selection.

Darwin was still researching and experimenting with his ideas on natural selection when he received a letter from Alfred Wallace describing a theory very similar to his own. This led to an immediate joint publication of both theories. Both Wallace and Darwin saw the history of life like a family tree, with each fork in the tree’s limbs being a common ancestor. The tips of the limbs represented modern species and the branches represented the common ancestors that are shared amongst many different species. To explain these relationships, Darwin said that all living things were related, and this meant that all life must be descended from a few forms, or even from a single common ancestor. He called this process "descent with modification".

Darwin published his theory of evolution by natural selection in On the Origin of Species in 1859. His theory means that all life, including humanity, is a product of continuing natural processes. The implication that all life on earth has a common ancestor has met with objections from some religious groups who believe even today that the different types of life are due to special creation. Their objections are in contrast to the level of support for the theory by more than 99 percent of those within the scientific community today.

Source of variation
Darwin’s theory of natural selection laid the groundwork for modern evolutionary theory, and his experiments and observations showed that the organisms in populations varied from each other, that some of these variations were inherited, and that these differences could be acted on by natural selection. However, he could not explain the source of these variations. Like many of his predecessors, Darwin mistakenly thought that heritable traits were a product of use and disuse, and that features acquired during an organism's lifetime could be passed on to its offspring. He looked for examples, such as large ground feeding birds getting stronger legs through exercise, and weaker wings from not flying until, like the ostrich, they could not fly at all. This misunderstanding was called the inheritance of acquired characters and was part of the theory of transmutation of species put forward in 1809 by Jean-Baptiste Lamarck. In the late 19th century this theory became known as Lamarckism. Darwin produced an unsuccessful theory he called pangenesis to try to explain how acquired characteristics could be inherited. In the 1880s August Weismann's experiments indicated that changes from use and disuse could not be inherited, and Lamarckism gradually fell from favor.

The missing information needed to help explain how new features could pass from a parent to its offspring was provided by the pioneering genetics work of Gregor Mendel. Mendel’s experiments with several generations of pea plants demonstrated that inheritance works by separating and reshuffling hereditary information during the formation of sex cells and recombining that information during fertilization. This is like mixing different hands of cards, with an organism getting a random mix of half of the cards from one parent, and half of the cards from the other. Mendel called the information factors; however, they later became known as genes. Genes are the basic units of heredity in living organisms. They contain the information that directs the physical development and behavior of organisms.

Genes are made of DNA, a long molecule that carries information. This information is encoded in the sequence of nucleotides in the DNA, just as the sequence of the letters in words carries information on a page. The genes are like short instructions built up of the "letters" of the DNA alphabet. Put together, the entire set of these genes gives enough information to serve as an "instruction manual" of how to build and run an organism. The instructions spelled out by this DNA alphabet can be changed, however, by mutations, and this may alter the instructions carried within the genes. Within the cell, the genes are carried in chromosomes, which are packages for carrying the DNA, with the genes arranged along them like beads on a string. It is the reshuffling of the chromosomes that results in unique combinations of genes in offspring. James Watson, co-discoverer of the structure of DNA

Although such mutations in DNA are random, natural selection is not a process of chance: the environment determines the probability of reproductive success. The end products of natural selection are organisms that are adapted to their present environments. Natural selection does not involve progress towards an ultimate goal. Evolution does not necessarily strive for more advanced, more intelligent, or more sophisticated life forms. For example, fleas (wingless parasites) are descended from a winged, ancestral scorpionfly, and snakes are lizards that no longer require limbs - although pythons still grow tiny structures that are the remains of their ancestor's hind legs. Organisms are merely the outcome of variations that succeed or fail, dependent upon the environmental conditions at the time.

Rapid environmental changes typically cause extinctions. Of all species that have existed on Earth, 99.9 percent are now extinct. Since life began on Earth, five major mass extinctions have led to large and sudden drops in the variety of species. The most recent, the Cretaceous–Tertiary extinction event, occurred 65 million years ago, and has attracted more attention than all others because it killed the dinosaurs.

Modern synthesis
The modern evolutionary synthesis was the outcome of a merger of several different scientific fields into a cohesive understanding of evolutionary theory. In the 1930s and 1940s, efforts were made to merge Darwin's theory of natural selection, research in heredity, and understandings of the fossil records into a unified explanatory model. The application of the principles of genetics to naturally occurring populations, by scientists such as Theodosius Dobzhansky and Ernst Mayr, advanced understanding of the processes of evolution. Dobzhansky's 1937 work Genetics and the Origin of Species was an important step in bridging the gap between genetics and field biology. Mayr, on the basis of an understanding of genes and direct observations of evolutionary processes from field research, introduced the biological species concept, which defined a species as a group of interbreeding or potentially interbreeding populations that are reproductively isolated from all other populations. The paleontologist George Gaylord Simpson helped to incorporate fossil research, which showed a pattern consistent with the branching and non-directional pathway of evolution of organisms predicted by the modern synthesis.

The modern synthesis emphasizes the importance of populations as the unit of evolution, the central role of natural selection as the most important mechanism of evolution, and the idea of gradualism to explain how large changes evolve as an accumulation of small changes over long periods of time.

Fossil record
Research in the field of paleontology, the study of fossils, supports the idea that all living organisms are related. Fossils provide evidence that accumulated changes in organisms over long periods of time have led to the diverse forms of life we see today. A fossil itself reveals the organism's structure and the relationships between present and extinct species, allowing paleontologists to construct a family tree for all of the life forms on earth.

Modern paleontology began with the work of Georges Cuvier (1769–1832). Cuvier noted that, in sedimentary rock each layer contained a specific group of fossils. The deeper layers, which he proposed to be older, contained simpler life forms. He noted that many forms of life from the past are no longer present today. One of Cuvier’s successful contributions to the understanding of the fossil record was establishing extinction as a fact. In an attempt to explain extinction, Cuvier proposed the idea of “revolutions” or catastrophism in which he speculated that geological catastrophes had occurred throughout the earth’s history, wiping out large numbers of species. Cuvier's theory of revolutions was later replaced by uniformitarian theories, notably those of James Hutton and Charles Lyell who proposed that the earth’s geological changes were gradual and consistent. However, current evidence in the fossil record supports the concept of mass extinctions. As a result, the general idea of catastrophism has re-emerged as a valid hypothesis for at least some of the rapid changes in life forms that appear in the fossil records.

A very large number of fossils have now been discovered and identified. These fossils serve as a chronological record of evolution. The fossil record provides examples of transitional species that demonstrate ancestral links between past and present life forms. One such transitional fossil is Archaeopteryx, an ancient organism that had the distinct characteristics of a reptile (such as a long, bony tail and conical teeth) yet also had characteristics of birds (such as feathers and a wishbone). The implication from such a find is that modern reptiles and birds arose from a common ancestor.

Comparative anatomy
The comparison of similarities between organisms of their form or appearance of parts, called their morphology, has long been a way to classify life into closely related groups. This can be done by comparing the structure of adult organisms in different species or by comparing the patterns of how cells grow, divide and even migrate during an organism's development.

In some cases, anatomical comparison of structures in the embryos of two or more species provides evidence for a shared ancestor that may not be obvious in the adult forms. As the embryo develops, these homologies can be lost to view, and the structures can take on different functions. Part of the basis of classifying the vertebrate group (which includes humans), is the presence of a tail (extending beyond the anus) and pharyngeal slits. Both structures appear during some stage of embryonic development but are not always obvious in the adult form.
 * Embryology

Because of the morphological similarities present in embryos of different species during development, it was once assumed that organisms re-enact their evolutionary history as an embryo. It was thought that human embryos passed through an amphibian then a reptilian stage before completing their development as mammals. The first stages of development are similar in broad groups of organisms. At very early stages, for instance, all vertebrates appear extremely similar, but do not exactly resemble any ancestral species. As development continues, specific features emerge from this basic pattern.

Homology includes a unique group of shared structures referred to as vestigial structures. Vestigial refers to anatomical parts that are of minimal, if any, value to the organism that possesses them. These apparently illogical structures are remnants of organs that played an important role in ancestral forms. Such is the case in whales, which have small vestigial bones that appear to be remnants of the leg bones of their ancestors which walked on land. Humans also have vestigial structures, including the ear muscles, the wisdom teeth, the appendix, the tail bone, body hair, goose bumps, and the semilunar fold in the corner of the eye.
 * Vestigial structures

Anatomical comparisons can be misleading, as not all anatomical similarities indicate a close relationship. Organisms that share similar environments will often develop similar physical features, a process known as convergent evolution. Both sharks and dolphins have similar body forms, yet are only distantly related – sharks are fish and dolphins are mammals. Such similarities are a result of both populations being exposed to the same selective pressures. Within both groups, changes that aid swimming have been favored. Thus, over time, they developed similar appearances (morphology), even though they are not closely related.
 * Convergent evolution

Molecular biology


Every living organism contains molecules of DNA, which carries genetic information. Genes are the pieces of DNA that carry this information, and they influence the properties of an organism. Genes determine an individual's general appearance and to some extent their behavior. If two organisms are closely related, their DNA will be very similar. On the other hand, the more distantly related two organisms are, the more differences they will have. For example, brothers are closely related and have very similar DNA, while cousins share a more distant relationship and have far more differences in their DNA. Similarities in DNA are used to determine the relationships between species in much the same manner as they are used to show relationships between individuals. For example, comparing chimpanzees with gorillas and humans shows that there is as much as a 96 percent similarity between the DNA of humans and chimps. Comparisons of DNA indicate that humans and chimpanzees are more closely related to each other than either species is to gorillas.

The field of Molecular phylogeny focuses on measuring the similarities in these molecules and using this information to work out how different types of organisms are related through evolution. These comparisons have allowed biologists to build a relationship tree of the evolution of life on earth. They have even allowed scientists to unravel the relationships between organisms whose common ancestors lived such a long time ago that no real similarities remain in the appearance of the organisms.

Co-evolution
Co-evolution is a process in which two or more species influence the evolution of each other. All organisms are influenced by life around them; however, in co-evolution there is evidence that genetically determined traits in each species directly resulted from the interaction between the two organisms.

An extensively documented case of co-evolution is the relationship between Pseudomyrmex, a type of ant, and the acacia, a plant that the ant uses for food and shelter. The relationship between the two is so intimate that it has led to the evolution of special structures and behaviors in both organisms. The ant defends the acacia against herbivores and clears the forest floor of the seeds from competing plants. In response, the plant has evolved swollen thorns that the ants use as shelter and special flower parts that the ants eat. Such co-evolution does not imply that the ants and the tree choose to behave in an altruistic manner. Rather, across a population small genetic changes in both ant and tree benefited each. The benefit gave a slightly higher chance of the characteristic being passed on to the next generation. Over time, successive mutations created the relationship we observe today.

Artificial selection


Artificial selection is the controlled breeding of domestic plants and animals. Humans determine which animal or plant will reproduce and which of the offspring will survive; thus, they determine which genes will be passed on to future generations. The process of artificial selection has had a significant impact on the evolution of domestic animals. For example, people have produced different types of dogs by controlled breeding. The differences in size between the Chihuahua and the Great Dane are the result of artificial selection. Despite their dramatically different physical appearance, they and all other dogs evolved from a few wolves domesticated by humans in what is now China less than 15,000 years ago.

Artificial selection has produced a wide variety of plants. In the case of maize (corn), recent genetic evidence suggests that domestication occurred 10,000 years ago in central Mexico. Prior to domestication, the edible portion of the wild form was small and difficult to collect. Today The Maize Genetics Cooperation • Stock Center maintains a collection of more than 10,000 genetic variations of maize that have arisen by random mutations and chromosomal variations from the original wild type. In artificial selection the new breed or variety that emerges is the one with random mutations attractive to humans, while in natural selection the surviving species is the one with random mutations useful to it in its non-human environment. In both natural and artificial selection the variations are a result of random mutations, and the underlying genetic processes are essentially the same. Darwin carefully observed the outcomes of artificial selection in animals and plants to form many of his arguments in support of natural selection. Much of his book On the Origin of Species was based on these observations of the many varieties of domestic pigeons arising from artificial selection. Darwin proposed that if humans could achieve dramatic changes in domestic animals in short periods, then natural selection, given millions of years, could produce the differences seen in living things today.

Speciation


Speciation is the lineage-splitting event that results in two separate species forming from a single common ancestral population. A widely accepted method of speciation is called allopatric speciation. Allopatric speciation begins when a population becomes geographically separated. Geological processes, such as the emergence of mountain ranges, the formation of canyons, or the flooding of land bridges by changes in sea level may result in separate populations. For speciation to occur, separation must be substantial, so that genetic exchange between the two populations is completely disrupted. In their separate environments, the genetically isolated groups follow their own unique evolutionary pathways. Each group will accumulate different mutations as well as be subjected to different selective pressures. The accumulated genetic changes may result in separated populations that can no longer interbreed if they are reunited. Barriers that prevent interbreeding are either prezygotic (prevent mating or fertilization) or postzygotic (barriers that occur after fertilization). If interbreeding is no longer possible, then they will be considered different species.

Usually the process of speciation is slow, occurring over very long time spans; thus direct observations within human life-spans are rare. However speciation has been observed in present day organisms, and past speciation events are recorded in fossils. Scientists have documented the formation of five new species of cichlid fishes from a single common ancestor that was isolated fewer than 5000 years ago from the parent stock in Lake Nagubago. The evidence for speciation in this case was morphology (physical appearance) and lack of natural interbreeding. These fish have complex mating rituals and a variety of colorations; the slight modifications introduced in the new species have changed the mate selection process and the five forms that arose could not be convinced to interbreed.

Rate of change
Two views exist concerning the rate of evolutionary change. Darwin and his contemporaries viewed evolution as a slow and gradual process. Evolutionary trees are based on the idea that profound differences in species are the result of many small changes that accumulate over long periods.

The view that evolution is gradual had its basis in the works of the geologist James Hutton (1726–1797) and his theory called "gradualism". Hutton's theory suggests that profound geological change was the cumulative product of a relatively slow continuing operation of processes which can still be seen in operation today, as opposed to catastrophism which promoted the idea that sudden changes had causes which can no longer be seen at work. A uniformitarian perspective was adopted for biological changes. Such a view can seem to contradict the fossil record, which shows evidence of new species appearing suddenly, then persisting in that form for long periods. The paleontologist Stephen Jay Gould (1940–2002) developed a model that suggests that evolution, although a slow process in human terms, undergoes periods of relatively rapid change over only a few thousand or million years, alternating with long periods of relative stability, a model called "punctuated equilibrium" which explains the fossil record without contradicting Darwin's ideas.

Unit of change
It is generally accepted that the unit of selection in evolution is the organism, and that natural selection serves to either enhance or reduce the reproductive potential of an individual. Reproductive success, therefore, can be measured by the volume of an organism's surviving offspring. The organism view has been challenged by a variety of biologists as well as philosophers. Richard Dawkins (born 1941) proposes that much insight can be gained if we look at evolution from the gene's point of view; that is, that natural selection operates as an evolutionary mechanism on genes as well as organisms. In his 1976 book The Selfish Gene, he explains:

Individuals are not stable things, they are fleeting. Chromosomes too are shuffled to oblivion, like hands of cards soon after they are dealt. But the cards themselves survive the shuffling. The cards are the genes. The genes are not destroyed by crossing-over; they merely change partners and march on. Of course they march on. That is their business. They are the replicators and we are their survival machines. When we have served our purpose we are cast aside. But genes are denizens of geological time: genes are forever.

Others view selection working on many levels, not just at a single level of organism or gene; for example, Stephen Jay Gould called for a hierarchical perspective on selection.

Summary
Several basic observations establish the theory of evolution, which explains the variety and relationship of all living things. There are genetic variations within a population of individuals. Some individuals, by chance, have features that allow them to survive and thrive better than their kind. The individuals that survive will be more likely to have offspring of their own. The offspring might inherit the useful feature.

Evolution is not a random process. While mutations are random, natural selection is not. Evolution is an inevitable result of imperfectly copying, self-replicating organisms reproducing over billions of years under the selective pressure of the environment. The outcome of evolution is not a perfectly designed organism. The outcome is simply an individual that can survive better and reproduce more successfully than its neighbors in a particular environment. Fossils, the genetic code, and the peculiar distribution of life on earth provide a record of evolution and demonstrate the common ancestry of all organisms, both living and long dead. Evolution can be directly observed in artificial selection, the selective breeding for certain traits of domestic animals and plants. The diverse breeds of cats, dogs, horses, and agricultural plants serve as examples of evolution.

Although some groups raise objections to the theory of evolution, the evidence of observation and experiments over a hundred years by thousands of scientists supports evolution. The result of four billion years of evolution is the diversity of life around us, with an estimated 1.75 million different species in existence today.