Evidence of common descent of living things has been discovered by scientists working in a variety of fields over many years. This evidence has demonstrated and verified the occurrence of evolution and provided a wealth of information on the natural processes by which the variety and diversity of life on Earth developed. This evidence supports the modern evolutionary synthesis, the current scientific theory that explains how and why life changes over time. Evolutionary biologists document the fact of common descent: making testable predictions, testing hypotheses, and developing theories that illustrate and describe its causes.
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from genetic detritus such as pseudogenes, regions ofDNA that are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration.
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 or homologous, demonstrating phylogenetic and ancestral relationships with other organism, 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. Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent.
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 island biogeography. Combined with the 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, like the spread of pesticide resistant forms of plants and insects provides evidence that evolution due to natural selection is an ongoing process in the natural world. Alongside this, are observed instances of the separation of populations of species into sets of new species (speciation). Speciation has been observed directly and indirectly 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 artificial selection of organisms—historically and currently—and other controlled experiments involving many of the topics in the article. This article explains the different types of evidence for evolution with common descent along with many specialized examples of each.
Genetics
One of the strongest evidences for common descent comes from the study of gene sequences. Comparative sequence analysis examines the relationship between the DNA sequences of different species,[1] 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 will have inherited that ancestor's DNA sequence, as well as 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.
Phylogenetic relationships also extend to a wide variety of nonfunctional 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.
[edit]Universal biochemical organisation and molecular variance patterns
All known extant (surviving) organisms are based on the same biochemical processes: genetic information encoded as nucleic acid (DNA, or RNA for viruses), transcribed into RNA, then translated intoproteins (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. A deeper understanding of developmental biology shows that common morphology is, in fact, the product of shared genetic elements.[2] For example, although camera-like eyes are believed to have evolved independently on many separate occasions,[3] they share a common set of light-sensing proteins (opsins), suggesting a common point of origin for all sighted creatures.[4][5][6] Another noteworthy example is the familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes.
[edit]DNA sequencing
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.[7][8] Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes.[9][10] 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 Eukaryotes.
[edit]Endogenous retroviruses
Endogenous retroviruses (or ERVs) are remnant sequences in the genome left from ancient viral infections in an organism. The retroviruses (or virogenes) are always passed on to the next generation of that organism which received the infection. This leaves the virogene left in the genome. Because this event is rare and random, finding identical chromosomal positions of a virogene in two different species suggests common ancestry.[11] See examples of humans and cats below.
[edit]Proteins
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. Phylogenetic analyses of protein sequences from various organisms produce similar trees of relationship between all organisms.[12] 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.[13]
[edit]Pseudogenes
Pseudogenes, also known as noncoding DNA, are extra DNA in a genome that do not get transcribed into RNA to synthesize proteins. Some of this noncoding DNA has known functions, but much of it has no known function and is called "Junk DNA". This is an example of a vestige since replicating these genes uses energy, making it a waste in many cases. Pseudogenes make up 99% of the human genome (1% working DNA).[14] A pseudogene can be produced when a coding gene accumulates mutations that prevent it from being transcribed, making it non-functional. But since it is not transcribed, it may disappear without affecting fitness, unless it has provided some new beneficial function as non-coding DNA. Non-functional pseudogenes may be passed on to later species, thereby labeling the later species as descended from the earlier species.
[edit]Other mechanisms
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. TheEndosymbiotic 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 ancienteukaryotic 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 been found in the protist Hatena: as a predator it engulfs a green algae cell, which subsequently behaves as an endosymbiont, nourishingHatena, which in turn loses its feeding apparatus and behaves as an autotroph.[15][16]
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.
[edit]Specific examples
[edit]Feline endogenous retroviruses
Cats (Felidae) present another example of virogene sequences in common descent. The standard phylogenetic tree for Felidae have smaller cats (Felis chaus, Felis silvestris, Felis nigripes, and Felis catus) diverging from larger cats such as the subfamily Pantherinae and other carnivores. The fact that small cats have an ERV where the larger cats do not suggests that the gene was inserted into the ancestor of the small cats after the larger cats had diverged.[17]
[edit]Chromosome 2 in humans
Evidence for the evolution of Homo sapiens from a common ancestor with chimpanzees is found in the number of chromosomes in humans as compared to all other members of Hominidae. All Hominidae (with the exception of humans) have 24 pairs of chromosomes. Humans have only 23 pairs. Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.[18][19]
The evidence for this includes:
- The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the common chimpanzee, has near-identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan.[20][21]
- The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere.[22]
- The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the middle.[23]
Chromosome 2 thus presents very strong evidence in favour of the common descent of humans and other apes. According to J. W. IJdo, "We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2."[23]
[edit]Cytochrome c
A classic example of biochemical evidence for evolution is the variance of the ubiquitous (i.e. all living organisms have it, because it performs very basic life functions) 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.
The primary structure of cytochrome c consists of a chain of about 100 amino acids. Many higher order organisms possess a chain of 104 amino acids.[24]
The cytochrome c molecule has been extensively studied for the glimpse it gives into evolutionary biology. Both chicken and turkeys have identical sequence homology (amino acid for amino acid), as do pigs, cows and sheep. Both humans and chimpanzees share the identical molecule, while rhesus monkeys share all but one of the amino acids:[25] the 66th amino acid is isoleucine in the former and threonine in the latter.[24]
What makes these homologous similarities particularly suggestive of common ancestry in the case of cytochrome C, in addition to the fact that the phylogenies derived from them match other phylogenies very well, is the high degree of functional redundancy of the cytochrome C molecule. The different existing configurations of amino acids do not significantly affect the functionality of the protein, which indicates that the base pair substitutions are not part of a directed design, but the result of random mutations that aren't subject to selection.[26]
[edit]Human endogenous retroviruses
Humans contain many ERVs that comprise nearly 8% of the genome.[27] Humans and chimps share seven different instances of virogenes while all primates share similar retroviruses congruent with phylogeny.[28]
[edit]Recent African origin of modern humans
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 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.[29]
Onsnap, now you know how it feels ^_^
