Evidence of common descent
|Part of the Biology series on|
|Mechanisms and processes|
|Research and history|
|Evolutionary biology fields|
|Biology Portal ·|
The wide range of evidence of common descent of living things strongly indicates the occurrence of evolution and provides a wealth of information on the natural processes by which the variety of life on Earth developed, supporting the modern evolutionary synthesis.
Fossils are important for estimating when various lineages developed. As fossilization is an uncommon occurrence, usually requiring hard body parts and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Evidence of organisms prior to the development of hard body parts such as shells, bones and teeth is especially scarce, but exists in the form of ancient microfossils, as well as impressions of various soft-bodied organisms.
Comparison of the genetic sequence of organisms has revealed that organisms that are phylogenetically close have a higher degree of sequence similarity than organisms that are phylogenetically distant. Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA that are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration. Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged at different stages of development, so it is possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor.
Evidence from genetics
Although it has only recently become available, the best evidence for common descent comes from the study of gene sequences. Comparative sequence analysis examines the relationship between the DNA sequences of different species, producing several lines of evidence that confirm Darwin's original hypothesis of common descent. If the the hypothesis of common descent is true, then species that share a common ancestor will have inherited that ancestor's DNA sequence. Notably they will have inherited mutations unique to that ancestor. More closely-related species will have a greater fraction of identical sequence and will have shared substitutions when compared to more distantly-related species.
The simplest and most powerful evidence is provided by phylogenetic reconstruction. Such reconstructions, especially when done using slowly-evolving protein sequences, are often quite robust and can be used to reconstruct a great deal of the evolutionary history of modern organisms (and even in some instances such as the recovered gene sequences of mammoths, Neanderthals or T. rex, the evolutionary history of extinct organisms). These reconstructed phylogenies recapitulate the relationships established through morphological and biochemical studies. The most detailed reconstructions have been performed on the basis of the mitochondrial genomes shared by all eukaryotic organisms, which are short and easy to sequence; the broadest reconstructions have been performed either using the sequences of a few very ancient proteins or by using ribosomal RNA sequence.
This evidence does not support the rival hypothesis that genetic similarity of two species is the product of common functional or structural requirements, and not common descent (for example, if there is one best way to produce a hoof, all hoofed creatures will share a genetic basis even if they are not related). However, phylogenetic relationships also extend to a wide variety of non-functional sequence elements, including repeats, transposons, pseudogenes, and mutations in protein-coding sequences that do not result in changes in amino-acid sequence. While a minority of these elements might later be found to harbor function, in aggregate they demonstrate that identity must be the product of common descent rather than common function.
Finally, a deeper understanding of developmental biology shows that common morphology is, in fact, the product of shared genetic elements. For example, although camera-like eyes are believed to have evolved independently on many separate occasions, they share a common set of light-sensing proteins (opsins), suggesting a common point of origin for all sighted creatures. Another noteworthy example is the familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes.
Evidence from paleontology
When organisms die, they often decompose rapidly or are consumed by scavengers, leaving no permanent evidences of their existence. However, occasionally, some organisms are preserved. The remains or traces of organisms from a past geologic age embedded in rocks by natural processes are called fossils. They are extremely important for understanding the evolutionary history of life on Earth, as they provide direct evidence of evolution and detailed information on the ancestry of organisms. Paleontology is the study of past life based on fossil records and their relations to different geologic time periods.
For fossilization to take place, the traces and remains of organisms must be quickly buried so that weathering and decomposition do not occur. Skeletal structures or other hard parts of the organisms are the most commonly occurring form of fossilized remains (Paul, 1998), (Behrensmeyer, 1980) and (Martin, 1999). There are also some trace "fossils" showing moulds, cast or imprints of some previous organisms.
As an animal dies, the organic materials gradually decay, such that the bones become porous. If the animal is subsequently buried in mud, mineral salts will infiltrate into the bones and gradually fill up the pores. The bones will harden into stones and be preserved as fossils. This process is known as petrification. If dead animals are covered by wind-blown sand, and if the sand is subsequently turned into mud by heavy rain or floods, the same process of mineral infiltration may occur. Apart from petrification, the dead bodies of organisms may be well preserved in ice, in hardened resin of coniferous trees (amber), in tar, or in anaerobic, acidic peat. Fossilization can sometimes be a trace, an impression of a form. Examples include leaves and footprints, the fossils of which are made in layers that then harden.
It is possible to find out how a particular group of organisms evolved by arranging its fossil records in a chronological sequence. Such a sequence can be determined because fossils are mainly found in sedimentary rock. Sedimentary rock is formed by layers of silt or mud on top of each other; thus, the resulting rock contains a series of horizontal layers, or strata. Each layer contains fossils which are typical for a specific time period during which they were made. The lowest strata contain the oldest rock and the earliest fossils, while the highest strata contain the youngest rock and more recent fossils.
A succession of animals and plants can also be seen from fossil records. By studying the number and complexity of different fossils at different stratigraphic levels, it has been shown that older fossil-bearing rocks contain fewer types of fossilized organisms, and they all have a simpler structure, whereas younger rocks contain a greater variety of fossils, often with increasingly complex structures.
In the past, geologists could only roughly estimate the ages of various strata and the fossils found. They did so, for instance, by estimating the time for the formation of sedimentary rock layer by layer. Today, by measuring the proportions of radioactive and stable elements in a given rock, the ages of fossils can be more precisely dated by scientists. This technique is known as radiometric dating.
Throughout the fossil record, many species that appear at an early stratigraphic level disappear at a later level. This is interpreted in evolutionary terms as indicating the times at which species originated and became extinct. Geographical regions and climatic conditions have varied throughout the Earth's history. Since organisms are adapted to particular environments, the constantly changing conditions favoured species which adapted to new environments through the mechanism of natural selection.
According to fossil records, some modern species of plants and animals are found to be almost identical to the species that lived in ancient geological ages. They are existing species of ancient lineages that have remained morphologically (and probably also physiologically) somewhat unchanged for a very long time. Consequently, they are called "living fossils" by laypeople. Examples of "living fossils" include the tuatara, the nautilus, the horseshoe crab, the coelacanth, the ginkgo, the Wollemi pine, and the metasequoia.
Extent of the Fossil Record
Despite the relative rarity of suitable conditions for fossilization, approximately 250,000 fossil species are known. The number of individual fossils this represents varies greatly from species to species, but many millions of fossils have been recovered: for instance, more than three million fossils from the last Ice Age have been recovered from the La Brea Tar Pits in Los Angeles. Many more fossils are still in the ground, in various geological formations known to contain a high fossil density, allowing estimates of the total fossil content of the formation to be made. An example of this occurs in South Africa's Beaufort Formation (part of the Karoo Supergroup, which covers most of South Africa), which is rich in vertebrate fossils, including therapsids (reptile/mammal transitional forms). It has been estimated that this formation contains 800 billion vertebrate fossils.
Evolution of the horse
Due to an almost-complete fossil record found in North American sedimentary deposits from the early Eocene to the present, the horse provides one of the best examples of evolutionary history (phylogeny).
This evolutionary sequence starts with a small animal called the Hyracotherium which lived in North America about 54 million years ago, then spread across to Europe and Asia. Fossil remains of Hyracotherium show it to have differed from the modern horse in three important respects: it was a small animal (the size of a fox), lightly built and adapted for running; the limbs were short and slender, and the feet elongated so that the digits were almost vertical, with four digits in the forelimbs and three digits in the hindlimbs; and the incisors were small, the molars having low crowns with rounded cusps covered in enamel.
The probable course of development of horses from Hyracotherium to Equus (the modern horse) involved at least 12 genera and several hundred species. The major trends seen in the development of the horse to changing environmental conditions may be summarized as follows:
- Increase in size (from 0.4 m to 1.5 m);
- Lengthening of limbs and feet;
- Reduction of lateral digits;
- Increase in length and thickness of the third digit;
- Increase in width of incisors;
- Replacement of premolars by molars; and
- Increases in tooth length, crown height of molars.
Fossilized plants found in different strata show that the marshy, wooded country in which Hyracotherium lived became gradually drier. Survival now depended on the head being in an elevated position for gaining a good view of the surrounding countryside, and on a high turn of speed for escape from predators, hence the increase in size and the replacement of the splayed-out foot by the hoofed foot. The drier, harder ground would make the original splayed-out foot unnecessary for support. The changes in the teeth can be explained by assuming that the diet changed from soft vegetation to grass. A dominant genus from each geological period has been selected to show the progressive development of the horse.
The fossil record is an important source for scientists when tracing the evolutionary history of organisms. However, because of limitations inherent in the record, there are not fine scales of intermediate forms between related groups of species. This lack of continuous fossils in the record is a major limitation in tracing the descent of biological groups. Furthermore, there are also much larger gaps between major evolutionary lineages. When transitional fossils are found that show intermediate forms in what had previously been a gap in knowledge, they are often popularly referred to as "missing links".
There is a gap of about 100 million years between the early Cambrian period and the later Ordovician period. The early Cambrian period was the period from which numerous fossils of sponges, cnidarians (e.g., jellyfish), echinoderms (e.g., eocrinoids), molluscs (e.g., snails) and arthropods (e.g., trilobites) are found. In the later Ordovician period, the first animal that really possessed the typical features of vertebrates, the Australian fish, Arandaspis appeared. Thus few, if any, fossils of an intermediate type between invertebrates and vertebrates have been found, although likely candidates include the Burgess Shale animal, Pikaia gracilens, and its Maotianshan shales relatives, Myllokunmingia, Yunnanozoon, Haikouella lanceolata, and Haikouichthys.
Some of the reasons for the incompleteness of fossil records are:
- In general, the probability that an organism becomes fossilized after death is very low;
- Some species or groups are less likely to become fossils because they are soft-bodied;
- Some species or groups are less likely to become fossils because they live (and die) in conditions that are not favourable for fossilization to occur in;
- Many fossils have been destroyed through erosion and tectonic movements;
- Some fossil remains are complete, but most are fragmentary;
- Some evolutionary change occurs in populations at the limits of a species' ecological range, and as these populations are likely to be small, the probability of fossilization is lower (see punctuated equilibrium);
- Similarly, when environmental conditions change, the population of a species is likely to be greatly reduced, such that any evolutionary change induced by these new conditions is less likely to be fossilized;
- Most fossils convey information about external form, but little about how the organism functioned;
- Using present-day biodiversity as a guide, this suggests that the fossils unearthed represent only a small fraction of the large number of species of organisms that lived in the past.
Evidence from comparative anatomy
Comparative study of the anatomy of groups of animals or plants reveals that certain structural features are basically similar. For example, the basic structure of all flowers consists of sepals, petals, stigma, style and ovary; yet the size, colour, number of parts and specific structure are different for each individual species.
Homologous structures and divergent (adaptive) evolution
If widely separated groups of organisms are originated from a common ancestry, they are expected to have certain basic features in common. The degree of resemblance between two organisms should indicate how closely related they are in evolution:
- Groups with little in common are assumed to have diverged from a common ancestor much earlier in geological history than groups which have a lot in common;
- In deciding how closely related two animals are, a comparative anatomist looks for structures that are fundamentally similar, even though they may serve different functions in the adult. Such structures are described as homologous and suggest a common origin.
- In cases where the similar structures serve different functions in adults, it may be necessary to trace their origin and embryonic development. A similar developmental origin suggests they are the same structure, and thus likely to be derived from a common ancestor.
When a group of organisms share a homologous structure which is specialized to perform a variety of functions in order to adapt different environmental conditions and modes of life are called adaptive radiation. The gradual spreading of organisms with adaptive radiation is known as divergent evolution.
The pattern of limb bones called pentadactyl limb is an example of homologous structures (Fig. 5a). It is found in all classes of tetrapods (i.e. from amphibians to mammals). It can even be traced back to the fins of certain fossil fishes from which the first amphibians are thought to have evolved. The limb has a single proximal bone (humerus), two distal bones (radius and ulna), a series of carpals (wrist bones), followed by five series of metacarpals (palm bones) and phalanges (digits). Throughout the tetrapods, the fundamental structures of pentadactyl limbs are the same, indicating that they originated from a common ancestor. But in the course of evolution, these fundamental structures have been modified. They have become superficially different and unrelated structures to serve different functions in adaptation to different environments and modes of life. This phenomenon is clearly shown in the forelimbs of mammals. For example:
- In the monkey, the forelimbs are much elongated to form a grasping hand for climbing and swinging among trees.
- In the pig, the first digit is lost, and the second and fifth digits are reduced. The remaining two digits are longer and stouter than the rest and bear a hoof for supporting the body.
- In the horse, the forelimbs are adapted for support and running by great elongation of the third digit bearing a hoof.
- The mole has a pair of short, spade-like forelimbs for burrowing.
- The anteater uses its enlarged third digit for tearing down ant hills and termite nests.
- In the whale, the forelimbs become flippers for steering and maintaining equilibrium during swimming.
- In the bat, the forelimbs have turned into wings for flying by great elongation of four digits, while the hook-like first digit remains free for hanging from trees.
The basic structures are the same, including a labrum (upper lip), a pair of mandibles, a hypopharynx (floor of mouth), a pair of maxillae, and a labium. These structures are enlarged and modified; others are reduced and lost. The modifications enable the insects to exploit a variety of food materials (Fig. 5b):
(A) Primitive state — biting and chewing: e.g. grasshopper. Strong mandibles and maxillae for manipulating food.
(C) Sucking: e.g. butterfly. Labrum reduced; mandibles lost; maxillae long forming sucking tube.
(D) Piercing and sucking, e.g. female mosquito. Labrum and maxillae form tube; mandibles form piercing stylets; labrum grooved to hold other parts.
Other arthropod appendages
Insect mouthparts and antennae are considered homologues of insect legs. Parallel developments are seen in some arachnids: The anterior pair of legs may be modified as analogues of antennae, particularly in whip scorpions, which walk on six legs. These developments provide support for the theory that complex modifications often arise by duplication of components, with the duplicates modified in different directions.
Analogous structures and convergent evolution
Under similar environmental conditions, fundamentally different structures in different groups of organisms may undergo modifications to serve similar functions. This phenomenon is called convergent evolution. Similar structures, physiological processes or mode of life in organisms apparently bearing no close phylogenetic links but showing adaptations to perform the same functions are described as analogous, for example:
- Wings of bats, birds and insects;
- the jointed legs of insects and vertebrates;
- tail fin of fish, whale and lobster;
- eyes of the vertebrates and cephalopod molluscs (squid and octopus). Fig. 6 illustrates difference between an inverted and non-inverted retina, the sensory cells lying beneath the nerve fibres. This results in the sensory cells being absent where the optic nerve is attached to the eye, thus creating a blind spot. The octopus eye has a non-inverted retina in which the sensory cells lie above the nerve fibres. There is therefore no blind spot in this kind of eye. Apart from this difference the two eyes are remarkably similar, an example of convergent evolution.
A further aspect of comparative anatomy is the presence of vestigial organs. Organs that are smaller and simpler in structure than corresponding parts in the ancestral species are called vestigial organs. They are usually degenerated or underdeveloped. The existence of vestigial organs can be explained in terms of changes in the environment or modes of life of the species. Those organs are thought to be functional in the ancestral species but have now become unnecessary and non-functional. Examples are the vestigial hind limbs of whales, the haltere (vestigial hind wings) of flies and mosquitos, vestigial wings of flightless birds such as ostriches, and the vestigial leaves of some xerophytes (e.g. cactus) and parasitic plants (e.g. dodder). It must be noted, however, that vestigial structures have lost the original function but may have another one. For example the halteres in dipterists help balance the insect while in flight and the wings of ostriches are used in mating rituals.
Evidence from geographical distribution
All organisms are adapted to their environment to a greater or lesser extent. If the abiotic and biotic factors within a habitat are capable of supporting a particular species in one geographic area, then one might assume that the same species would be found in a similar habitat in a similar geographic area, e.g. in Africa and South America. This is not the case. Plant and animal species are discontinuously distributed throughout the world:
- Africa has short-tailed (Old World) monkeys, elephants, lions and giraffes.
- South America has long-tailed monkeys, cougars, jaguars and llamas.
Even greater differences can be found if Australia is taken into consideration, though it occupies the same latitude as much of South America and Africa. Marsupials like the kangaroo, the wallaby, and the wombat make up over 80 percent of Australia's indigenous mammal population. By contrast, marsupials are totally absent from Africa and are only represented by the opossum in South America and the Virginia Opossum in North America:
- The echidna and platypus, the only living representatives of primitive egg-laying mammals (monotremes), can be found only in Australia and are totally absent in the rest of the world.
- On the other hand, Australia has very few placental mammals and most of these either migrated from elsewhere (e.g. bats) or were introduced by human beings (e.g. rabbits).
The main groups of modern mammal arose in Northern Hemisphere and subsequently migrated to three major directions:
- to South America via the land bridge in the Bering Strait and Isthmus of Panama; A large number of families of South American marsupials became extinct as a result of competition with these North American counterparts.
- to Africa via the Strait of Gibraltar; and
- to Australia via South East Asia to which it was at one time connected by land
The shallowness of the Bering Strait would have made the passage of animals between two northern continents a relatively easy matter, and it explains the present-day similarity of the two faunas. But once they had got down into the southern continents, they presumably became isolated from each other by various types of barriers.
- The submersion of the Isthmus of Panama: isolates the South American fauna.
- The Mediterranean Sea and the North African desert: partially isolate the African fauna.
- The submersion of the original connection between Australia and South East Asia: isolates the Australian fauna.
Once isolated, the animals in each continent have shown adaptive radiation (Fig. 7) to evolve along their own lines.
Evidence for migration and isolation
The fossil record for the camel indicated that evolution of camels started in North America, from which they migrated across the Bering Strait into Asia and hence to Africa, and through the Isthmus of Panama into South America. Once isolated, they evolved along their own lines, giving the modern camel in Asia and Africa and llama in South America.
The same kinds of fossils are found from areas known to be adjacent to one another in the past but which, through the process of continental drift, are now in widely divergent geographic locations. For example, fossils of the same types of ancient amphibians, arthropods and ferns are found in South America, Africa, India, Australia and Antarctica, which can be dated to the Paleozoic Era, at which time these regions were united as a single landmass called Gondwana.  Sometimes the descendants of these organisms can be identified and show unmistakable similarity to each other, even though they now inhabit very different regions and climates.
Oceanic island distribution
Most small isolated islands only have native species that could have arrived by air or water; like birds, insects and turtles. The few large mammals present today were brought by human settlers in boats. Plant life on remote and recent volcanic islands like Hawaii could have arrived as airborne spores or as seeds in the droppings of birds. After the explosion of Krakatoa a century ago and the emergence of a steaming, lifeless remnant island called Anak Krakatoa (child of Krakatoa), plants arrived within months and within a year there were moths and spiders that had arrived by air. The island is now ecologically hard to distinguish from those around it that have been there for millions of years.
Evidence from comparative physiology and biochemistry
Universal biochemical organisation
All known extant organisms are based on the same fundamental biochemical organisation: genetic information encoded as nucleic acid (DNA, or RNA for viruses), transcribed into RNA, then translated into proteins (that is, polymers of amino acids) by highly conserved ribosomes. Perhaps most tellingly, the Genetic Code (the "translation table" between DNA and amino acids) is the same for almost every organism, meaning that a piece of DNA in a bacterium codes for the same amino acid as in a human cell. ATP is used as energy currency by all extant life.
Molecular variance patterns
A classic example of biochemical evidence for evolution is the variance of the protein Cytochrome c in living cells. The variance of cytochrome c of different organisms is measured in the number of differing amino acids, each differing amino acid being a result of a base pair substitution, a mutation. If each differing amino acid is assumed to be the result of one base pair substitution, it can be calculated how long ago the two species diverged by multiplying the number of base pair substitutions by the estimated time it takes for a substituted base pair of the cytochrome c gene to be successfully passed on. For example, if the average time it takes for a base pair of the cytochrome c gene to mutate is N years, the number of amino acids making up the cytochrome c protein in monkeys differ by one from that of humans, this leads to the conclusion that the two species diverged N years ago.
Comparison of the DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas, and 6.6% from baboons. Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes. The sequence of the 16S ribosomal RNA gene, a vital gene encoding a part of the ribosome, was used to find the broad phylogenetic relationships between all extant life. The analysis, originally done by Carl Woese, resulted in the three-domain system, arguing for two major splits in the early evolution of life. The first split led to modern Bacteria and the subsequent split led to modern Archaea and Eukaryote.
The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase, are found in everything from the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions. Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent. The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right- or left-handed molecular chirality, the simplest hypothesis is that the choice was made randomly by early organisms and passed on to all extant life through common descent. Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, "dead" genes which steadily accumulate mutations.
There is also a large body of molecular evidence for a number of different mechanisms for large evolutionary changes, among them: genome and gene duplication, which facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints; horizontal gene transfer, the process of transferring genetic material to another cell that is not an organism's offspring, allowing for species to acquire beneficial genes from each other; and recombination, capable of reassorting large numbers of different alleles and of establishing reproductive isolation. The Endosymbiotic theory explains the origin of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells, as the incorporation of an ancient prokaryotic cell into ancient eukaryotic cell. Rather than evolving eukaryotic organelles slowly, this theory offers a mechanism for a sudden evolutionary leap by incorporating the genetic material and biochemical composition of a separate species. Evidence supporting this mechanism has recently been found in the protist Hatena: as a predator it engulfs a green algae cell, which subsequently behaves as an endosymbiont, nourishing Hatena, which in turn loses its feeding apparatus and behaves as an autotroph.
Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor or by detecting their physical manifestations. As an example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.
Out of Africa hypothesis of human evolution
Mathematical models of evolution, pioneered by the likes of Sewall Wright, Ronald Fisher and J. B. S. Haldane and extended via diffusion theory by Motoo Kimura, allow predictions about the genetic structure of evolving populations. Direct examination of the genetic structure of modern populations via DNA sequencing has recently allowed verification of many of these predictions. For example, the Out of Africa theory of human origins, which states that modern humans developed in Africa and a small sub-population migrated out (undergoing a population bottleneck), implies that modern populations should show the signatures of this migration pattern. Specifically, post-bottleneck populations (Europeans and Asians) should show lower overall genetic diversity and a more uniform distribution of allele frequencies compared to the African population. Both of these predictions are borne out by actual data from a number of studies.
Evidence from antibiotic and pesticide resistance
The development and spread of antibiotic resistant bacteria, like the spread of pesticide resistant forms of plants and insects is evidence for evolution of species, and of change within species. Thus the appearance of vancomycin resistant Staphylococcus aureus, and the danger it poses to hospital patients is a direct result of evolution through natural selection. The rise of Shigella strains resistant to the synthetic antibiotic class of sulfonamides also demonstrates the generation of new information as an evolutionary process. Similarly, the appearance of DDT resistance in various forms of Anopheles mosquitoes, and the appearance of myxomatosis resistance in breeding rabbit populations in Australia, are all evidence of the existence of evolution in situations of evolutionary selection pressure in species in which generations occur rapidly.
Evidence from studies of complex iteration
Computer science allows the iteration of self changing complex systems to be studied, allowing a mathematical understanding of the nature of the processes behind evolution; providing evidence for the hidden causes of known evolutionary events. The evolution of specific cellular mechanisms like spliceosomes that can turn the cell's genome into a vast workshop of billions of interchangeable parts that can create tools that create tools that create tools that create us can be studied for the first time in an exact way.
For example, Christoph Adami et al. make this point in Evolution of biological complexity:
- To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon," within a fixed environment, genomic complexity is forced to increase. 
For example, David J. Earl and Michael W. Deem make this point in Evolvability is a selectable trait:
- Not only has life evolved, but life has evolved to evolve. That is, correlations within protein structure have evolved, and mechanisms to manipulate these correlations have evolved in tandem. The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution. Sensibly, rapid or extreme environmental change leads to selection for greater evolvability. This selection is not forbidden by causality and is strongest on the largest-scale moves within the mutational hierarchy. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. For example, the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low-fidelity polymerases during somatic hypermutation. A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of influenza A. 
"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins."  Evolutionary molecular engineering, also called directed evolution or in vitro molecular evolution involves the iterated cycle of mutation, multiplication with recombination, and selection of the fittest of individual molecules (proteins, DNA, and RNA). Natural evolution can be relived showing us possible paths from catalytic cycles based on proteins to based on RNA to based on DNA.    
Evidence from speciation
One example of evolution at work is the case of the hawthorn fly, Rhagoletis pomonella, also known as the apple maggot fly, which appears to be undergoing sympatric speciation. Different populations of hawthorn fly feed on different fruits. A distinct population emerged in North America in the 19th century some time after apples, a non-native species, were introduced. This apple-feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. The current hawthorn feeding population does not normally feed on apples. Some evidence, such as the fact that six out of thirteen allozyme loci are different, that hawthorn flies mature later in the season and take longer to mature than apple flies; and that there is little evidence of interbreeding (researchers have documented a 4-6% hybridization rate) suggests that this is occurring. The emergence of the new hawthorn fly is an example of evolution in progress.
- Two sources: 'Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees'. and 'Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes' " "
- The picture labeled "Human Chromosome 2 and its analogs in the apes" in the article Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry is literally a picture of a link in humans that links two separate chromosomes in the nonhuman apes creating a single chromosome in humans. It is considered a missing link, and the ape-human connection is of particular interest. Also, while the term originally referred to fossil evidence, this too is a trace from the past corresponding to some living beings which when alive were the physical embodiment of this link.
- The New York Times report Still Evolving, Human Genes Tell New Story, based on A Map of Recent Positive Selection in the Human Genome, states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.
- Pseudogene evolution and natural selection for a compact genome. ""
- Okamoto N, Inouye I. (2005). "A secondary symbiosis in progress". Science. 310 (5746): 287. doi:10.1126/science.1116125.
- Okamoto N (October 2006). "Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition". Protist. 157 (4): 401–419. doi:10.1016/j.protis.2006.05.011. Unknown parameter
- Tanaka T, Hashimoto H. (1989). "Drug-resistance and its transferability of Shigella strains isolated in 1986 in Japan". Kansenshogaku Zasshi. 63 (1): 15–26.
- Feder; et al. (2003). "Evidence for inversion polymorphism related to sympatric host race formation in the apple maggot fly, Rhagoletis pomonella". Genetics. 163 (3): 939–953.
- Berlocher, S.H. and G.L. Bush. 1982. An electrophoretic analysis of Rhagoletis (Diptera: Tephritidae) phylogeny. Systematic Zoology 31:136-155; Berlocher, S.H. and J.L. Feder. 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annual Review of Entomology 47:773-815; Bush, G.L. 1969. Sympatric host race formation and speciation in frugivorous flies of the genus Rhagoletis (Diptera: Tephritidae). Evolution 23:237-251; Prokopy, R.J., S.R. Diehl and S.S. Cooley. 1988. Behavioral evidence for host races in Rhagoletis pomonella flies. Oecologia 76:138-147. Proc. Natl. Acad. Sci. USA - Vol. 94, pp. 11417-11421, October 1997 - Evolution article Selective maintenance of allozyme differences among sympatric host races of the apple maggot fly.
- Darwin, Charles November 24 1859. On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street. 502 pages. Reprinted: Gramercy (May 22, 1995). ISBN 0-517-12320-7
- Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0-465-04426-3
- Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
- Williams, G.C. (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought. Princeton, N.J.: Princeton University Press.
- Biological science, Oxford, 2002.
- CJ Clegg, 1999, Genetics and Evolution, John Murray. ISBN 0-7195-7552-4
- Y.K. Ho, 2004, Advanced-level Biology for Hong Kong, Manhattan Press. ISBN 962-990-635-X
- Paul, Christopher R. C. (1998) The Adequacy of the Fossil Record, John Wiley & Sons, ISBN 0-471-96988-5
- Behrensmeyer, Anna K. (1980) Fossils in the making: Vertebrate taphonomy and paleoecology, University of Chicago Press, ISBN 0-226-04169-7
- Martin, Ronald E. et al. eds. (1999) Taphonomy: A Process Approach, Cambridge University Press, ISBN 0-521-59833-8
- 29+ Evidences for Macroevolution: The Scientific Case for Common Descent
- National Academies Evolution Resources
- Evolution by Natural Selection — An introduction to the logic of the theory of evolution by natural selection
- Evolution — Provided by PBS.
- Howstuffworks.com — How Evolution Works
- Evolution News from Genome News Network (GNN)
- National Academy Press: Teaching About Evolution and the Nature of Science
- Transitional Vertebrate Fossils FAQ