Evidence of common descent
Evidence of common descent of living organisms has been discovered by scientists researching in a variety of disciplines over many decades, demonstrating that all life on Earth comes from a single ancestor. This forms an important part of the evidence on which evolutionary theory rests, demonstrates that evolution does occur, and illustrates the processes that created Earth's biodiversity. It supports the modern evolutionary synthesis—the current scientific theory that explains how and why life changes over time. Evolutionary biologists document evidence of common descent, all the way back to the last universal common ancestor, by developing testable predictions, testing hypotheses, and constructing theories that illustrate and describe its causes.
Comparison of the DNA genetic sequences of organisms has revealed that organisms that are phylogenetically close have a higher degree of DNA sequence similarity than organisms that are phylogenetically distant. Genetic fragments such as pseudogenes, regions of DNA that are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration from cumulative mutations support common descent alongside the universal biochemical organization and molecular variance patterns found in all organisms. Additional genetic information conclusively supports the relatedness of life and has allowed scientists to develop phylogenetic trees: a construction of organisms' evolutionary relatedness. It has also led to the development of molecular clock techniques to date taxon divergence times and to calibrate these with the fossil record.
Fossils are important for estimating when various lineages developed in geologic time. 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. The comparative study of the anatomy of groups of animals shows structural features that are fundamentally similar, demonstrating phylogenetic and ancestral relationships with other organisms, most especially when compared with fossils of ancient extinct organisms. Vestigial structures and comparisons in embryonic development are largely a contributing factor in anatomical resemblance in concordance with common descent. Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms' physiology and biochemistry. 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 animal coloration was gathered by some of Darwin's contemporaries; camouflage, mimicry, and warning coloration are all readily explained by natural selection. Special cases like the seasonal changes in the plumage of the ptarmigan, camouflaging it against snow in winter and against brown moorland in summer provide compelling evidence that selection is at work. Further evidence comes from the field of biogeography because evolution with common descent provides the best and most thorough explanation for a variety of facts concerning the geographical distribution of plants and animals across the world. This is especially obvious in the field of insular biogeography. Combined with the well-established geological theory of plate tectonics, common descent provides a way to combine facts about the current distribution of species with evidence from the fossil record to provide a logically consistent explanation of how the distribution of living organisms has changed over time.
The development and spread of antibiotic resistant bacteria provides evidence that evolution due to natural selection is an ongoing process in the natural world. Natural selection is ubiquitous in all research pertaining to evolution, taking note of the fact that all of the following examples in each section of the article document the process. Alongside this are observed instances of the separation of populations of species into sets of new species. Speciation has been observed in the lab and in nature. Multiple forms of such have been described and documented as examples for individual modes of speciation. Furthermore, evidence of common descent extends from direct laboratory experimentation with the selective breeding of organisms—historically and currently—and other controlled experiments involving many of the topics in the article. This article summarizes the varying disciplines that provide the evidence for evolution and the common descent of all life on Earth, accompanied by numerous and specialized examples, indicating a compelling consilience of evidence.
Evidence from comparative physiology and biochemistry
Genetics
One of the strongest evidences for common descent comes from 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 hypothesis of common descent is true, then species that share a common ancestor inherited that ancestor's DNA sequence, as well as mutations unique to that ancestor. More closely related species have a greater fraction of identical sequence and shared substitutions compared to more distantly related species.File:HMS Beagle by Conrad Martens.jpg|thumb|right|Figure 1a: While on board HMS Beagle, Charles Darwin collected numerous specimens, many new to science, which supported his later theory of evolution by natural selection.
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. 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.
Phylogenetic relationships extend to a wide variety of nonfunctional sequence elements, including repeats, transposons, pseudogenes, and mutations in protein-coding sequences that do not change the 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.
Universal biochemical organisation and molecular variance patterns
All known extant organisms are based on the same biochemical processes: genetic information encoded as nucleic acid, transcribed into RNA, then translated into proteins by highly conserved ribosomes. Perhaps most tellingly, the genetic code 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. 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, suggesting a common point of origin for all sighted creatures. Another example is the familiar vertebrate body plan, whose structure is controlled by the homeobox family of genes.DNA sequencing
Comparison of 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 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 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 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 Eukaryotes.Some DNA sequences are shared by very different organisms. It has been predicted by the theory of evolution that the differences in such DNA sequences between two organisms should roughly resemble both the biological difference between them according to their anatomy and the time that had passed since these two organisms have separated in the course of evolution, as seen in fossil evidence. The rate of accumulating such changes should be low for some sequences, namely those that code for critical RNA or proteins, and high for others that code for less critical RNA or proteins; but for every specific sequence, the rate of change should be roughly constant over time. These results have been experimentally confirmed. Two examples are DNA sequences coding for rRNA, which is highly conserved, and DNA sequences coding for fibrinopeptides, amino acid chains discarded during the formation of fibrin, which are highly non-conserved.