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1.1.1 Fossil evidence
Fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils can often be deduced based upon the geologic context in which they are found. Some fossils bear a resemblance to organisms alive today, while others are radically different. Fossils have been used to determine at what time a lineage developed, and can be used to demonstrate the continuity between two different lineages through transitional forms . Paleontologists investigate evolution largely through analysis of fossils.
1.1.2 Genetic evidence
Comparison of the genetic sequence of organisms reveals that organisms that are phylogenetically close have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, human genes are more than 99% identical to their nearest genetic relative, chimpanzees, slightly less so for gorillas, and only 80% identical to baboons. Sequence comparison is considered such a robust measure that it is sometimes used to correct mistakes in the phylogenetic tree, in instances where other evidence is scarce.
Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA which are ortholog ous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration.
1.2 The emergence of novel traits
Geneticists have studied how traits emerge and how they are passed to succeeding generations. In Darwin's time, there was no widely accepted mechanism for inheritance. Today most inherited variation is traced to discrete, persistent entities called genes. Genes are encoded in linear molecules called DNA. Changes in DNA are commonly called mutations. Furthermore, mutations may have little phenotypic effect in isolation but create new traits when combined in an organism through genetic recombination. Genetic recombination is produced both by the fusion of cells of opposite sexes, and by the transfer of genetic material into an intact cell, which occurs in bacterial conjugation and transformation.
Researchers are also investigating heritable variation that is not connected to variations in DNA sequences that influence standard DNA replication. The processes that produce these variations leave the genetic information intact and are often reversible. This is called epigenetic inheritance and may include phenomena such as DNA methylation, prions, and structural inheritance. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this is shown to be the case, then some instances of evolution would lie outside of the framework that Darwin established, which avoided any connection between environmental signals and the production of heritable variation.
In addition to the mechanisms described above, the origin of novel traits may also be attributable to self-organizing properties at the level of the physics and chemistry of the organism (which some hold to be a violation of "strict" Darwinism). Self-organization in this context would refer to traits that were not directly encoded in the genome but rather would always be expected to be present in a wide class of particular biological systems. In this view, as expressed by Stuart Kauffman, natural selection "selects" only particular classes of systems, which happen to include systems which generate such "order for free" (Kauffman also calls this property "anti-chaos"). Several specific mechanisms to enable "order for free" such as the robustness of genetic regulatory networks, the spontaneous self-sustaining order of chemical reactions as autocatalytic sets and the properties of the RNA genotype-to-phenotype map (in this case, the RNA-sequence-to-RNA-shape mapping), have been cautiously incorporated as part of a workable theory as it applies to evolution. However, the entire program as outlined by Kauffman remains a matter for debate.
1.3 Differential survival of traits
Differential survival of traits in a population means that some characteristics will become more frequent while others occur less or are lost. There are four known processes that affect the survival of a characteristic; or, more specifically, the frequency of an allele:
The production and redistribution of variation is produced by three of the four agents of evolution: mutation, genetic drift, and gene flow. Natural selection, in turn, acts on the variation produced by these agents.
