biological evolution

Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms, and molecules.

The theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book ''On the Origin of Species''. Evolution by natural selection is established by observable facts about living organisms: (1) more offspring are often produced than can possibly survive (2) traits vary among individuals with respect to their morphology, physiology, and behaviour ( phenotypic variation); (3) different traits confer different rates of survival and reproduction (differential fitness); and (4) traits can be passed from generation to generation ( heritability of fitness). In successive generations, members of a population are therefore more likely to be replaced by the offspring of parents with favourable characteristics. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis concluded Darwinian evolution acts on Mendelian genetic variation.

All life on Earth shares a last universal common ancestor (LUCA), which lived approximately 3.5–3.8 billion years ago. The fossil record includes a progression from early biogenic graphite to microbial mat fossils to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped by repeated formations of new species (speciation), changes within species ( anagenesis), and loss of species (extinction) throughout the evolutionary history of life on Earth. Morphological and biochemical traits are more similar among species that share a more recent common ancestor, and these traits can be used to reconstruct phylogenetic trees.

Evolutionary biologists have continued to study various aspects of evolution by forming and testing hypotheses as well as constructing theories based on evidence from the field or laboratory and on data generated by the methods of mathematical and theoretical biology. Their discoveries have influenced not just the development of biology but numerous other scientific and industrial fields, including agriculture, medicine, and computer science.

Heredity

Evolution in organisms occurs through changes in heritable traits—the inherited characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents. Inherited traits are controlled by genes and the complete set of genes within an organism's genome (genetic material) is called its genotype.

The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment. As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specifies the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes).

Some heritable changes cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems. DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three-dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level. Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalisation. Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.

Sources of variation

Evolution can occur if there is genetic variation within a population. Variation comes from mutations in the genome, reshuffling of genes through sexual reproduction and migration between populations (gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species. However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.

An individual organism's phenotype results from both its genotype and the influence of the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation. The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixation—when it either disappears from the population or replaces the ancestral allele entirely.

Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variation would be rapidly lost, making evolution by natural selection implausible. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.

Mutation

Mutations are changes in the DNA sequence of a cell's genome and are the ultimate source of genetic variation in all organisms. When mutations occur, they may alter the product of a gene, or prevent the gene from functioning, or have no effect. Based on studies in the fly ''Drosophila melanogaster'', it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome. Extra copies of genes are a major source of the raw material needed for new genes to evolve. This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors. For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function. Other types of mutations can even generate entirely new genes from previously noncoding DNA, a phenomenon termed de novo gene birth.

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions ( exon shuffling). When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions. For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyse one step in the overall process, like a step in an assembly line.

One example of mutation is wild boar piglets. They are camouflage colored and show a characteristic pattern of dark and light longitudinal stripes. However, mutations in '' melanocortin 1 receptor'' (''MC1R'') disrupt the pattern. The majority of pig breeds carry ''MC1R'' mutations disrupting wild-type color and different mutations causing dominant black color of the pigs.

Sex and recombination

In asexual organisms, genes are inherited together, or ''linked'', as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes. Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles. Sex usually increases genetic variation and may increase the rate of evolution.

The two-fold cost of sex was first described by John Maynard Smith. The first cost is that in sexually dimorphic species only one of the two sexes can bear young. This cost does not apply to hermaphroditic species, like most plants and many invertebrates. The second cost is that any individual who reproduces sexually can only pass on 50% of its genes to any individual offspring, wit