Regulation of gene expression

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Regulation_of_gene_expression

Regulation of gene expression by a hormone receptor

Diagram showing at which stages in the DNA-mRNA-protein pathway expression can be controlled

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.

In multicellular organisms, gene regulation drives cellular differentiation and morphogenesis in the embryo, leading to the creation of different cell types that possess different gene expression profiles from the same genome sequence. Although this does not explain how gene regulation originated, evolutionary biologists include it as a partial explanation of how evolution works at a molecular level, and it is central to the science of evolutionary developmental biology ("evo-devo").

Regulated stages of gene expression

Any step of gene expression may be modulated, from signaling to transcription to post-translational modification of a protein. The following is a list of stages where gene expression is regulated, where the most extensively utilized point is transcription initiation, the first stage in transcription:

• Signal transduction
• Chromatin, chromatin remodeling, chromatin domains
• Transcription
• Post-transcriptional modification
• RNA transport
• Translation
• mRNA degradation

Modification of DNA

Histone tails and their function in chromatin formation

In eukaryotes, the accessibility of large regions of DNA can depend on its chromatin structure, which can be altered as a result of histone modifications directed by DNA methylation, ncRNA, or DNA-binding protein. Hence these modifications may up or down regulate the expression of a gene. Some of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation.

Structural

Transcription of DNA is dictated by its structure. In general, the density of its packing is indicative of the frequency of transcription. Octameric protein complexes called histones together with a segment of DNA wound around the eight histone proteins (together referred to as a nucleosome) are responsible for the amount of supercoiling of DNA, and these complexes can be temporarily modified by processes such as phosphorylation or more permanently modified by processes such as methylation. Such modifications are considered to be responsible for more or less permanent changes in gene expression levels.

Chemical

Methylation of DNA is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "CpG islands" when densely clustered). Analysis of the pattern of methylation in a given region of DNA (which can be a promoter) can be achieved through a method called bisulfite mapping. Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences are analyzed by DNA sequencing or by methods developed to quantify SNPs, such as Pyrosequencing (Biotage) or MassArray (Sequenom), measuring the relative amounts of C/T at the CG dinucleotide. Abnormal methylation patterns are thought to be involved in oncogenesis.

Histone acetylation is also an important process in transcription. Histone acetyltransferase enzymes (HATs) such as CREB-binding protein also dissociate the DNA from the histone complex, allowing transcription to proceed. Often, DNA methylation and histone deacetylation work together in gene silencing. The combination of the two seems to be a signal for DNA to be packed more densely, lowering gene expression.

Regulation of transcription

Main article: Transcriptional regulation

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is essentially turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, which obstructs the RNA polymerase from binding to the promoter and making lactase. Bottom: The gene is turned on. Lactose is inhibiting the repressor, allowing the RNA polymerase to bind with the promoter, and express the genes, which synthesize lactase. Eventually, the lactase will digest all of the lactose, until there is none to bind to the repressor. The repressor will then bind to the operator, stopping the manufacture of lactase.

Regulation of transcription thus controls when transcription occurs and how much RNA is created. Transcription of a gene by RNA polymerase can be regulated by several mechanisms. Specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters, making it more or less likely to bind to them (i.e., sigma factors used in prokaryotic transcription). Repressors bind to the Operator, coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene. The image to the right demonstrates regulation by a repressor in the lac operon. General transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase to transcribe the mRNA. Activators enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene. Activators do this by increasing the attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly by changing the structure of the DNA. Enhancers are sites on the DNA helix that are bound by activators in order to loop the DNA bringing a specific promoter to the initiation complex. Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date). Silencers are regions of DNA sequences that, when bound by particular transcription factors, can silence expression of the gene.

Regulation by RNA

RNA can be an important regulator of gene activity, e.g. by microRNA (miRNA), antisense-RNA, or long non-coding RNA (lncRNA). LncRNAs differ from mRNAs in the sense that they have specified subcellular locations and functions. They were first discovered to be located in the nucleus and chromatin, and the localizations and functions are highly diverse now. Some still reside in chromatin where they interact with proteins. While this lncRNA ultimately affects gene expression in neuronal disorders such as Parkinson, Huntington, and Alzheimer disease, others, such as, PNCTR(pyrimidine-rich non-coding transcriptors), play a role in lung cancer. Given their role in disease, lncRNAs are potential biomarkers and may be useful targets for drugs or gene therapy, although there are no approved drugs that targert lncRNAs yet. The number of lncRNAs in the human genome remains poorly defined, but some estimates range from 16,000 to 100,000 lnc genes.

Epigenetic gene regulation

Overview of Epigenetic mechanisms.

Epigenetics refers to the modification of genes that is not changing the DNA or RNA sequence. Epigenetic modifications are also a key factor in influencing gene expression. They occur on genomic DNA and histones and their chemical modifications regulate gene expression in a more efficient manner. There are several modifications of DNA (usually methylation) and more than 100 modifications of RNA in mammalian cells.” Those modifications result in altered protein binding to DNA and a change in RNA stability and translation efficiency.

Special cases in human biology and disease

Regulation of transcription in cancer

Main article: Regulation of transcription in cancer

In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG sites are methylated the gene becomes silenced. Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, transcriptional silencing may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see regulation of transcription in cancer). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered expression of microRNAs. In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-expressed microRNA-182 than by hypermethylation of the BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers).

Regulation of transcription in addiction

One of the cardinal features of addiction is its persistence. The persistent behavioral changes appear to be due to long-lasting changes, resulting from epigenetic alterations affecting gene expression, within particular regions of the brain. Drugs of abuse cause three types of epigenetic alteration in the brain. These are (1) histone acetylations and histone methylations, (2) DNA methylation at CpG sites, and (3) epigenetic downregulation or upregulation of microRNAs. (See Epigenetics of cocaine addiction for some details.)

Chronic nicotine intake in mice alters brain cell epigenetic control of gene expression through acetylation of histones. This increases expression in the brain of the protein FosB, important in addiction. Cigarette addiction was also studied in about 16,000 humans, including never smokers, current smokers, and those who had quit smoking for up to 30 years. In blood cells, more than 18,000 CpG sites (of the roughly 450,000 analyzed CpG sites in the genome) had frequently altered methylation among current smokers. These CpG sites occurred in over 7,000 genes, or roughly a third of known human genes. The majority of the differentially methylated CpG sites returned to the level of never-smokers within five years of smoking cessation. However, 2,568 CpGs among 942 genes remained differentially methylated in former versus never smokers. Such remaining epigenetic changes can be viewed as “molecular scars” that may affect gene expression.

In rodent models, drugs of abuse, including cocaine, methamphetamine, alcohol and tobacco smoke products, all cause DNA damage in the brain. During repair of DNA damages some individual repair events can alter the methylation of DNA and/or the acetylations or methylations of histones at the sites of damage, and thus can contribute to leaving an epigenetic scar on chromatin.

Such epigenetic scars likely contribute to the persistent epigenetic changes found in addiction.

Regulation of transcription in learning and memory

DNA methylation is the addition of a methyl group to the DNA that happens at cytosine. The image shows a cytosine single ring base and a methyl group added on to the 5 carbon. In mammals, DNA methylation occurs almost exclusively at a cytosine that is followed by a guanine.

In mammals, methylation of cytosine (see Figure) in DNA is a major regulatory mediator. Methylated cytosines primarily occur in dinucleotide sequences where cytosine is followed by a guanine, a CpG site. The total number of CpG sites in the human genome is approximately 28 million. and generally about 70% of all CpG sites have a methylated cytosine.

The identified areas of the human brain are involved in memory formation.

In a rat, a painful learning experience, contextual fear conditioning, can result in a life-long fearful memory after a single training event. Cytosine methylation is altered in the promoter regions of about 9.17% of all genes in the hippocampus neuron DNA of a rat that has been subjected to a brief fear conditioning experience. The hippocampus is where new memories are initially stored.

Methylation of CpGs in a promoter region of a gene represses transcription while methylation of CpGs in the body of a gene increases expression. TET enzymes play a central role in demethylation of methylated cytosines. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene.

When contextual fear conditioning is applied to a rat, more than 5,000 differentially methylated regions (DMRs) (of 500 nucleotides each) occur in the rat hippocampus neural genome both one hour and 24 hours after the conditioning in the hippocampus. This causes about 500 genes to be up-regulated (often due to demethylation of CpG sites in a promoter region) and about 1,000 genes to be down-regulated (often due to newly formed 5-methylcytosine at CpG sites in a promoter region). The pattern of induced and repressed genes within neurons appears to provide a molecular basis for forming the first transient memory of this training event in the hippocampus of the rat brain.

Post-transcriptional regulation

Main article: Post-transcriptional regulation

After the DNA is transcribed and mRNA is formed, there must be some sort of regulation on how much the mRNA is translated into proteins. Cells do this by modulating the capping, splicing, addition of a Poly(A) Tail, the sequence-specific nuclear export rates, and, in several contexts, sequestration of the RNA transcript. These processes occur in eukaryotes but not in prokaryotes. This modulation is a result of a protein or transcript that, in turn, is regulated and may have an affinity for certain sequences.

Three prime untranslated regions and microRNAs

Main article: Three prime untranslated region

Main article: MicroRNA

Three prime untranslated regions (3'-UTRs) of messenger RNAs (mRNAs) often contain regulatory sequences that post-transcriptionally influence gene expression. Such 3'-UTRs often contain both binding sites for microRNAs (miRNAs) as well as for regulatory proteins. By binding to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3'-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA.

The 3'-UTR often contains miRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent motifs within 3'-UTRs. Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs.

As of 2014, the miRBase web site, an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic species. Of these, 1,881 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target mRNAs (affecting expression of several hundred genes). Freidman et al. estimate that >45,000 miRNA target sites within human mRNA 3'-UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs.

Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs. Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold).

The effects of miRNA dysregulation of gene expression seem to be important in cancer. For instance, in gastrointestinal cancers, a 2015 paper identified nine miRNAs as epigenetically altered and effective in down-regulating DNA repair enzymes.

The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depressive disorder, Parkinson's disease, Alzheimer's disease and autism spectrum disorders.

Regulation of translation

Main article: Translational regulation

The translation of mRNA can also be controlled by a number of mechanisms, mostly at the level of initiation. Recruitment of the small ribosomal subunit can indeed be modulated by mRNA secondary structure, antisense RNA binding, or protein binding. In both prokaryotes and eukaryotes, a large number of RNA binding proteins exist, which often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer). Some transcripts act as ribozymes and self-regulate their expression.

Examples of gene regulation

• Enzyme induction is a process in which a molecule (e.g., a drug) induces (i.e., initiates or enhances) the expression of an enzyme.
• The induction of heat shock proteins in the fruit fly Drosophila melanogaster.
• The Lac operon is an interesting example of how gene expression can be regulated.
• Viruses, despite having only a few genes, possess mechanisms to regulate their gene expression, typically into an early and late phase, using collinear systems regulated by anti-terminators (lambda phage) or splicing modulators (HIV).
• Gal4 is a transcriptional activator that controls the expression of GAL1, GAL7, and GAL10 (all of which code for the metabolic of galactose in yeast). The GAL4/UAS system has been used in a variety of organisms across various phyla to study gene expression.

Developmental biology

Main article: Evolutionary developmental biology

A large number of studied regulatory systems come from developmental biology. Examples include:

• The colinearity of the Hox gene cluster with their nested antero-posterior patterning
• Pattern generation of the hand (digits - interdigits): the gradient of sonic hedgehog (secreted inducing factor) from the zone of polarizing activity in the limb, which creates a gradient of active Gli3, which activates Gremlin, which inhibits BMPs also secreted in the limb, results in the formation of an alternating pattern of activity as a result of this reaction–diffusion system.
• Somitogenesis is the creation of segments (somites) from a uniform tissue (Pre-somitic Mesoderm). They are formed sequentially from anterior to posterior. This is achieved in amniotes possibly by means of two opposing gradients, Retinoic acid in the anterior (wavefront) and Wnt and Fgf in the posterior, coupled to an oscillating pattern (segmentation clock) composed of FGF + Notch and Wnt in antiphase.
• Sex determination in the soma of a Drosophila requires the sensing of the ratio of autosomal genes to sex chromosome-encoded genes, which results in the production of sexless splicing factor in females, resulting in the female isoform of doublesex.

Circuitry

Main article: Gene regulatory network

Up-regulation and down-regulation

Up-regulation is a process which occurs within a cell triggered by a signal (originating internal or external to the cell), which results in increased expression of one or more genes and as a result the proteins encoded by those genes. Conversely, down-regulation is a process resulting in decreased gene and corresponding protein expression.

• Up-regulation occurs, for example, when a cell is deficient in some kind of receptor. In this case, more receptor protein is synthesized and transported to the membrane of the cell and, thus, the sensitivity of the cell is brought back to normal, reestablishing homeostasis.
• Down-regulation occurs, for example, when a cell is overstimulated by a neurotransmitter, hormone, or drug for a prolonged period of time, and the expression of the receptor protein is decreased in order to protect the cell (see also tachyphylaxis).

Inducible vs. repressible systems

Gene regulation works using operators and repressors in bacteria.

Gene Regulation can be summarized by the response of the respective system:

• Inducible systems - An inducible system is off unless there is the presence of some molecule (called an inducer) that allows for gene expression. The molecule is said to "induce expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.
• Repressible systems - A repressible system is on except in the presence of some molecule (called a corepressor) that suppresses gene expression. The molecule is said to "repress expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.

The GAL4/UAS system is an example of both an inducible and repressible system. Gal4 binds an upstream activation sequence (UAS) to activate the transcription of the GAL1/GAL7/GAL10 cassette. On the other hand, a MIG1 response to the presence of glucose can inhibit GAL4 and therefore stop the expression of the GAL1/GAL7/GAL10 cassette.

Theoretical circuits

• Repressor/Inducer: an activation of a sensor results in the change of expression of a gene
• negative feedback: the gene product downregulates its own production directly or indirectly, which can result in
  • keeping transcript levels constant/proportional to a factor
  • inhibition of run-away reactions when coupled with a positive feedback loop
  • creating an oscillator by taking advantage in the time delay of transcription and translation, given that the mRNA and protein half-life is shorter
• positive feedback: the gene product upregulates its own production directly or indirectly, which can result in
  • signal amplification
  • bistable switches when two genes inhibit each other and both have positive feedback
  • pattern generation

Study methods

Schematic karyogram of a human, showing an overview of the human genome on G banding, which is a method that includes Giemsa staining, wherein the lighter staining regions are generally more transcriptionally active, whereas darker regions are more inactive.

Further information: Karyotype

For DNA and RNA methods, see nucleic acid methods.

For protein methods, see protein methods.

In general, most experiments investigating differential expression used whole cell extracts of RNA, called steady-state levels, to determine which genes changed and by how much. These are, however, not informative of where the regulation has occurred and may mask conflicting regulatory processes (see post-transcriptional regulation), but it is still the most commonly analysed (quantitative PCR and DNA microarray).

When studying gene expression, there are several methods to look at the various stages. In eukaryotes these include:

• The local chromatin environment of the region can be determined by ChIP-chip analysis by pulling down RNA Polymerase II, Histone 3 modifications, Trithorax-group protein, Polycomb-group protein, or any other DNA-binding element to which a good antibody is available.
• Epistatic interactions can be investigated by synthetic genetic array analysis
• Due to post-transcriptional regulation, transcription rates and total RNA levels differ significantly. To measure the transcription rates nuclear run-on assays can be done and newer high-throughput methods are being developed, using thiol labelling instead of radioactivity.
• Only 5% of the RNA polymerised in the nucleus exits, and not only introns, abortive products, and non-sense transcripts are degradated. Therefore, the differences in nuclear and cytoplasmic levels can be seen by separating the two fractions by gentle lysis.
• Alternative splicing can be analysed with a splicing array or with a tiling array (see DNA microarray).
• All in vivo RNA is complexed as RNPs. The quantity of transcripts bound to specific protein can be also analysed by RIP-Chip. For example, DCP2 will give an indication of sequestered protein; ribosome-bound gives and indication of transcripts active in transcription (although a more dated method, called polysome fractionation, is still popular in some labs)
• Protein levels can be analysed by Mass spectrometry, which can be compared only to quantitative PCR data, as microarray data is relative and not absolute.
• RNA and protein degradation rates are measured by means of transcription inhibitors (actinomycin D or α-Amanitin) or translation inhibitors (Cycloheximide), respectively.

Molecular genetics

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Molecular_genetics
 

Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens.

The field of study is based on the merging of several sub-fields in biology: classical Mendelian inheritance, cellular biology, molecular biology, biochemistry, and biotechnology. It integrates these disciplines to explore things like genetic inheritance, gene regulation and expression, and the molecular mechanism behind various life processes.

A key goal of molecular genetics is to identify and study genetic mutations. Researchers search for mutations in a gene or induce mutations in a gene to link a gene sequence to a specific phenotype. Therefore molecular genetics is a powerful methodology for linking mutations to genetic conditions that may aid the search for treatments of various genetics diseases.

History

The discovery of DNA as the blueprint for life and breakthroughs in molecular genetics research came from the combined works of many scientists. In 1869, chemist Johann Friedrich Miescher, who was researching the composition of white blood cells, discovered and isolated a new molecule that he named nuclein from the cell nucleus, which would ultimately be the first discovery of the molecule DNA that was later determined to be the molecular basis of life. He determined it was composed of hydrogen, oxygen, nitrogen and phosphorus. Biochemist Albrecht Kossel identified nuclein as a nucleic acid and provided its name deoxyribonucleic acid (DNA). He continued to build on that by isolating the basic building blocks of DNA and RNA; made up of the nucleotides: adenine, guanine, thymine, cytosine. and uracil. His work on nucleotides earned him a Nobel Prize in Physiology.

In the early 1900s, Gregor Mendel, who became known as one of the fathers of genetics, made great contributions to the field of genetics through his various experiments with pea plants where he was able to discover the principles of inheritance such as recessive and dominant traits, without knowing what genes where composed of. In the mid 19th century, anatomist Walther Flemming, discovered what we now know as chromosomes and the separation process they undergo through mitosis. His work along with Theodor Boveri first came up with the Chromosomal Theory of Inheritance, which helped explain some of the patterns Mendel had observed much earlier.

For molecular genetics to develop as a discipline, several scientific discoveries were necessary.  The discovery of DNA as a means to transfer the genetic code of life from one cell to another and between generations was essential for identifying the molecule responsible for heredity. Molecular genetics arose initially from studies involving genetic transformation in bacteria. In 1944 Avery, McLeod and McCarthy isolated DNA from a virulent strain of S. pneumoniae, and using just this DNA were able to convert a harmless strain to virulence. They called the uptake, incorporation and expression of DNA by bacteria "transformation". This finding suggested that DNA is the genetic material of bacteria. Bacterial transformation is often induced by conditions of stress, and the function of transformation appears to be repair of genomic damage.

In 1950, Erwin Chargaff derived rules that offered evidence of DNA being the genetic material of life. These were "1) that the base composition of DNA varies between species and 2) in natural DNA molecules, the amount of adenine (A) is equal to the amount of thymine (T), and the amount of guanine (G) is equal to the amount of cytosine (C)." These rules, known as Chargaff's rules, helped to understand of molecular genetics. In 1953 Francis Crick and James Watson, building upon the X-ray crystallography work done by Rosalind Franklin and Maurice Wilkins, were able to derive the 3-D double helix structure of DNA.

The phage group was an informal network of biologists centered on Max Delbrück that contributed substantially to molecular genetics and the origins of molecular biology during the period from about 1945 to 1970. The phage group took its name from bacteriophages, the bacteria-infecting viruses that the group used as experimental model organisms. Studies by molecular geneticists affiliated with this group contributed to understanding how gene-encoded proteins function in DNA replication, DNA repair and DNA recombination, and on how viruses are assembled from protein and nucleic acid components (molecular morphogenesis). Furthermore, the role of chain terminating codons was elucidated. One noteworthy study was performed by Sydney Brenner and collaborators using "amber" mutants defective in the gene encoding the major head protein of bacteriophage T4. This study demonstrated the co-linearity of the gene with its encoded polypeptide, thus providing strong evidence for the "sequence hypothesis" that the amino acid sequence of a protein is specified by the nucleotide sequence of the gene determining the protein. 

The isolation of a restriction endonuclease in E. coli by Arber and Linn in 1969 opened the field of genetic engineering. Restriction enzymes were used to linearize DNA for separation by electrophoresis and Southern blotting allowed for the identification of specific DNA segments via hybridization probes. In 1971, Berg utilized restriction enzymes to create the first recombinant DNA molecule and first recombinant DNA plasmid.  In 1972, Cohen and Boyer created the first recombinant DNA organism by inserting recombinant DNA plasmids into E. coli, now known as bacterial transformation, and paved the way for molecular cloning.  The development of DNA sequencing techniques in the late 1970s, first by Maxam and Gilbert, and then by Frederick Sanger, was pivotal to molecular genetic research and enabled scientists to begin conducting genetic screens to relate genotypic sequences to phenotypes. Polymerase chain reaction (PCR) using Taq polymerase, invented by Mullis in 1985, enabled scientists to create millions of copies of a specific DNA sequence that could be used for transformation or manipulated using agarose gel separation. A decade later, the first whole genome was sequenced (Haemophilus influenzae), followed by the eventual sequencing of the human genome via the Human Genome Project in 2001. The culmination of all of those discoveries was a new field called genomics that links the molecular structure of a gene to the protein or RNA encoded by that segment of DNA and the functional expression of that protein within an organism. Today, through the application of molecular genetic techniques, genomics is being studied in many model organisms and data is being collected in computer databases like NCBI and Ensembl. The computer analysis and comparison of genes within and between different species is called bioinformatics, and links genetic mutations on an evolutionary scale.

Central dogma

This image shows an example of the central dogma using a DNA strand being transcribed then translated and showing important enzymes used in the processes.

The central dogma plays a key role in the study of molecular genetics. The central dogma states that DNA replicates itself, DNA is transcribed into RNA, and RNA is translated into proteins. Along with the central dogma, the genetic code is used in understanding how RNA is translated into proteins. Replication of DNA and transcription from DNA to mRNA occurs in the nucleus while translation from RNA to proteins occurs in the ribosome. The genetic code is made of four interchangeable parts othe DNA molecules, called "bases": adenine, cytosine, uracil (in RNA; thymine in DNA), and guanine and is redundant, meaning multiple combinations of these base pairs (which are read in triplicate) produce the same amino acid. Proteomics and genomics are fields in biology that come out of the study of molecular genetics and the central dogma.

Structure of DNA

An organism's genome is made up by its entire set of DNA and is responsible for its genetic traits, function and development. The composition of DNA itself is an essential component to the field of molecular genetics; it is the basis of how DNA is able to store genetic information, pass it on, and be in a format that can be read and translated.

DNA is a double stranded molecule, with each strand oriented in an antiparallel fashion. Nucleotides are the building blocks of DNA, each composed of a sugar molecule, a phosphate group and one of four nitrogenous bases: adenine, guanine, cytosine, and thymine. A single strand of DNA is held together by covalent bonds, while the two antiparallel strands are held together by hydrogen bonds between the nucleotide bases. Adenine binds with thymine and cytosine binds with guanine. It is these four base sequences that form the genetic code for all biological life and contains the information for all the proteins the organism will be able to synthesize.

Its unique structure allows DNA to store and pass on biological information across generations during cell division. At cell division, cells must be able to copy its genome and pass it on to daughter cells. This is possible due to the double-stranded structure of DNA because one strand is complementary to its partner strand, and therefore each of these strands can act as a template strand for the formation of a new complementary strand. This is why the process of DNA replication is known as a semiconservative process.

Techniques

Forward genetics

Forward genetics is a molecular genetics technique used to identify genes or genetic mutations that produce a certain phenotype. In a genetic screen, random mutations are generated with mutagens (chemicals or radiation) or transposons and individuals are screened for the specific phenotype. Often, a secondary assay in the form of a selection may follow mutagenesis where the desired phenotype is difficult to observe, for example in bacteria or cell cultures. The cells may be transformed using a gene for antibiotic resistance or a fluorescent reporter so that the mutants with the desired phenotype are selected from the non-mutants.

Mutants exhibiting the phenotype of interest are isolated and a complementation test may be performed to determine if the phenotype results from more than one gene. The mutant genes are then characterized as dominant (resulting in a gain of function), recessive (showing a loss of function), or epistatic (the mutant gene masks the phenotype of another gene). Finally, the location and specific nature of the mutation is mapped via sequencing. Forward genetics is an unbiased approach and often leads to many unanticipated discoveries, but may be costly and time consuming. Model organisms like the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the zebrafish Danio rerio have been used successfully to study phenotypes resulting from gene mutations.

An example of forward genetics in C. elegans (a nematode) using mutagenesis

Reverse genetics

Diagram illustrating the development process of avian flu vaccine by reverse genetics techniques

Reverse genetics is the term for molecular genetics techniques used to determine the phenotype resulting from an intentional mutation in a gene of interest. The phenotype is used to deduce the function of the un-mutated version of the gene. Mutations may be random or intentional changes to the gene of interest. Mutations may be a missense mutation caused by nucleotide substitution, a nucleotide addition or deletion to induce a frameshift mutation, or a complete addition/deletion of a gene or gene segment. The deletion of a particular gene creates a gene knockout where the gene is not expressed and a loss of function results (e.g. knockout mice). Missense mutations may cause total loss of function or result in partial loss of function, known as a knockdown. Knockdown may also be achieved by RNA interference (RNAi). Alternatively, genes may be substituted into an organism's genome (also known as a transgene) to create a gene knock-in and result in a gain of function by the host. Although these techniques have some inherent bias regarding the decision to link a phenotype to a particular function, it is much faster in terms of production than forward genetics because the gene of interest is already known.

Molecular genetic tools

Molecular genetics is a scientific approach that utilizes the fundamentals of genetics as a tool to better understand the molecular basis of a disease and biological processes in organisms. Below are some tools readily employed by researchers in the field.

Microsatellites

Microsatellites or single sequence repeats (SSRS) are short repeating segment of DNA composed to 6 nucleotides at a particular location on the genome that are used as genetic marker. Researchers can analyze these microsatellites in techniques such DNA fingerprinting and paternity testing since these repeats are highly unique to individuals/families. a can also be used in constructing genetic maps and to studying genetic linkage to locate the gene or mutation responsible for specific trait or disease. Microsatellites can also be applied to population genetics to study comparisons between groups.

Genome-wide association studies

Genome-wide association studies (GWAS) are a technique that relies on single nucleotide polymorphisms (SNPs) to study genetic variations in populations that can be associated with a particular disease. The Human Genome Project mapped the entire human genome and has made this approach more readily available and cost effective for researchers to implement. In order to conduct a GWAS researchers use two groups, one group that has the disease researchers are studying and another that acts as the control that does not have that particular disease. DNA samples are obtained from participants and their genome can then be derived through lab machinery and quickly surveyed to compare participants and look for SNPs that can potentially be associated with the disease. This technique allows researchers to pinpoint genes and locations of interest in the human genome that they can then further study to identify that cause of the disease.

Karyotyping

Karyotyping allows researchers to analyze chromosomes during metaphase of mitosis, when they are in a condensed state. Chromosomes are stained and visualized through a microscope to look for any chromosomal abnormalities. This technique can be used to detect congenital genetic disorder such as down syndrome, identify gender in embryos, and diagnose some cancers that are caused by chromosome mutations such as translocations.

Modern applications

Genetic engineering

Genetic engineering is an emerging field of science, and researcher are able to leverage molecular genetic technology to modify the DNA of organisms and create genetically modified and enhanced organisms for industrial, agricultural and medical purposes. This can be done through genome editing techniques, which can involve modifying base pairings in a DNA sequence, or adding and deleting certain regions of DNA.

Gene editing

Gene editing allows scientists to alter/edit an organism's DNA. One way to due this is through the technique Crispr/Cas9, which was adapted from the genome immune defense that is naturally occurring in bacteria. This technique relies on the protein Cas9 which allows scientists to make a cut in strands of DNA at a specific location, and it uses a specialized RNA guide sequence to ensure the cut is made in the proper location in the genome. Then scientists use DNAs repair pathways to induce changes in the genome; this technique has wide implications for disease treatment.

Personalized medicine

Molecular genetics has wide implications in medical advancement and understanding the molecular basis of a disease allows the opportunity for more effective diagnostic and therapies. One of the goals of the field is personalized medicine, where an individual's genetics can help determine the cause and tailor the cure for a disease they are afflicted with and potentially allow for more individualized treatment approaches which could be more effective. For example, certain genetic variations in individuals could make them more receptive to a particular drug while other could have a higher risk of adverse reaction to treatments. So this information would allow researchers and clinicals to make the most informed decisions about treatment efficacy for patients rather than the standard trial and error approach.

Forensic genetics

Forensic genetics plays an essential role for criminal investigations through that use of various molecular genetic techniques. One common technique is DNA fingerprinting which is done using a combination of molecular genetic techniques like polymerase chain reaction (PCR) and gel electrophoresis. PCR is a technique that allows a target DNA sequence to be amplified, meaning even a tiny quantity of DNA from a crime scene can be extracted and replicated many times to provide a sufficient amount of material for analysis. Gel electrophoresis allows the DNA sequence to be separated based on size, and the pattern that is derived is known as DNA fingerprinting and is unique to each individual. This combination of molecular genetic techniques allows a simple DNA sequence to be extracted, amplified, analyzed and compared with others and is a standard technique used in forensics.

Transitional fossil

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Transitional_fossil

Archaeopteryx is one of the most famous transitional fossils and gives evidence for the evolution of birds from theropod dinosaurs.

A transitional fossil is any fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group. This is especially important where the descendant group is sharply differentiated by gross anatomy and mode of living from the ancestral group. These fossils serve as a reminder that taxonomic divisions are human constructs that have been imposed in hindsight on a continuum of variation. Because of the incompleteness of the fossil record, there is usually no way to know exactly how close a transitional fossil is to the point of divergence. Therefore, it cannot be assumed that transitional fossils are direct ancestors of more recent groups, though they are frequently used as models for such ancestors.

In 1859, when Charles Darwin's On the Origin of Species was first published, the fossil record was poorly known. Darwin described the perceived lack of transitional fossils as "the most obvious and gravest objection which can be urged against my theory," but he explained it by relating it to the extreme imperfection of the geological record. He noted the limited collections available at the time but described the available information as showing patterns that followed from his theory of descent with modification through natural selection. Indeed, Archaeopteryx was discovered just two years later, in 1861, and represents a classic transitional form between earlier, non-avian dinosaurs and birds. Many more transitional fossils have been discovered since then, and there is now abundant evidence of how all classes of vertebrates are related, including many transitional fossils. Specific examples of class-level transitions are: tetrapods and fish, birds and dinosaurs, and mammals and "mammal-like reptiles".

The term "missing link" has been used extensively in popular writings on human evolution to refer to a perceived gap in the hominid evolutionary record. It is most commonly used to refer to any new transitional fossil finds. Scientists, however, do not use the term, as it refers to a pre-evolutionary view of nature.

Evolutionary and phylogenetic taxonomy

Transitions in phylogenetic nomenclature

Main article: Phylogenetic nomenclature

See also: Evolutionary taxonomy

Traditional spindle diagram showing the vertebrates classes "budding" off from each other. Transitional fossils typically represent animals from near the branching points.

In evolutionary taxonomy, the prevailing form of taxonomy during much of the 20th century and still used in non-specialist textbooks, taxa based on morphological similarity are often drawn as "bubbles" or "spindles" branching off from each other, forming evolutionary trees. Transitional forms are seen as falling between the various groups in terms of anatomy, having a mixture of characteristics from inside and outside the newly branched clade.

With the establishment of cladistics in the 1990s, relationships commonly came to be expressed in cladograms that illustrate the branching of the evolutionary lineages in stick-like figures. The different so-called "natural" or "monophyletic" groups form nested units, and only these are given phylogenetic names. While in traditional classification tetrapods and fish are seen as two different groups, phylogenetically tetrapods are considered a branch of fish. Thus, with cladistics there is no longer a transition between established groups, and the term "transitional fossils" is a misnomer. Differentiation occurs within groups, represented as branches in the cladogram.

In a cladistic context, transitional organisms can be seen as representing early examples of a branch, where not all of the traits typical of the previously known descendants on that branch have yet evolved. Such early representatives of a group are usually termed "basal taxa" or "sister taxa," depending on whether the fossil organism belongs to the daughter clade or not.

Transitional versus ancestral

A source of confusion is the notion that a transitional form between two different taxonomic groups must be a direct ancestor of one or both groups. The difficulty is exacerbated by the fact that one of the goals of evolutionary taxonomy is to identify taxa that were ancestors of other taxa. However, because evolution is a branching process that produces a complex bush pattern of related species rather than a linear process producing a ladder-like progression, and because of the incompleteness of the fossil record, it is unlikely that any particular form represented in the fossil record is a direct ancestor of any other. Cladistics deemphasizes the concept of one taxonomic group being an ancestor of another, and instead emphasizes the identification of sister taxa that share a more recent common ancestor with one another than they do with other groups. There are a few exceptional cases, such as some marine plankton microfossils, where the fossil record is complete enough to suggest with confidence that certain fossils represent a population that was actually ancestral to a later population of a different species. But, in general, transitional fossils are considered to have features that illustrate the transitional anatomical features of actual common ancestors of different taxa, rather than to be actual ancestors.

Prominent examples

Archaeopteryx

Main article: Origin of birds

A historic 1904 reconstruction of Archæopteryx

Archaeopteryx is a genus of theropod dinosaur closely related to the birds. Since the late 19th century, it has been accepted by palaeontologists, and celebrated in lay reference works, as being the oldest known bird, though a study in 2011 has cast doubt on this assessment, suggesting instead that it is a non-avialan dinosaur closely related to the origin of birds.

It lived in what is now southern Germany in the Late Jurassic period around 150 million years ago, when Europe was an archipelago in a shallow warm tropical sea, much closer to the equator than it is now. Similar in shape to a European magpie, with the largest individuals possibly attaining the size of a raven, Archaeopteryx could grow to about 0.5 metres (1.6 ft) in length. Despite its small size, broad wings, and inferred ability to fly or glide, Archaeopteryx has more in common with other small Mesozoic dinosaurs than it does with modern birds. In particular, it shares the following features with the deinonychosaurs (dromaeosaurs and troodontids): jaws with sharp teeth, three fingers with claws, a long bony tail, hyperextensible second toes ("killing claw"), feathers (which suggest homeothermy), and various skeletal features. These features make Archaeopteryx a clear candidate for a transitional fossil between dinosaurs and birds, making it important in the study both of dinosaurs and of the origin of birds.

The first complete specimen was announced in 1861, and ten more Archaeopteryx fossils have been found since then. Most of the eleven known fossils include impressions of feathers—among the oldest direct evidence of such structures. Moreover, because these feathers take the advanced form of flight feathers, Archaeopteryx fossils are evidence that feathers began to evolve before the Late Jurassic.

Australopithecus afarensis

Main articles: Australopithecus afarensis and Human evolution

See also: List of human evolution fossils

A. afarensis - walking posture

The hominid Australopithecus afarensis represents an evolutionary transition between modern bipedal humans and their quadrupedal ape ancestors. A number of traits of the A. afarensis skeleton strongly reflect bipedalism, to the extent that some researchers have suggested that bipedality evolved long before A. afarensis. In overall anatomy, the pelvis is far more human-like than ape-like. The iliac blades are short and wide, the sacrum is wide and positioned directly behind the hip joint, and there is clear evidence of a strong attachment for the knee extensors, implying an upright posture.

While the pelvis is not entirely like that of a human (being markedly wide, or flared, with laterally orientated iliac blades), these features point to a structure radically remodelled to accommodate a significant degree of bipedalism. The femur angles in toward the knee from the hip. This trait allows the foot to fall closer to the midline of the body, and strongly indicates habitual bipedal locomotion. Present-day humans, orangutans and spider monkeys possess this same feature. The feet feature adducted big toes, making it difficult if not impossible to grasp branches with the hindlimbs. Besides locomotion, A. afarensis also had a slightly larger brain than a modern chimpanzee (the closest living relative of humans) and had teeth that were more human than ape-like.

Pakicetids, Ambulocetus

Main article: Evolution of cetaceans

 

Reconstruction of Pakicetus

 

Skeleton of Ambulocetus natans

The cetaceans (whales, dolphins and porpoises) are marine mammal descendants of land mammals. The pakicetids are an extinct family of hoofed mammals that are the earliest whales, whose closest sister group is Indohyus from the family Raoellidae. They lived in the Early Eocene, around 53 million years ago. Their fossils were first discovered in North Pakistan in 1979, at a river not far from the shores of the former Tethys Sea. Pakicetids could hear under water, using enhanced bone conduction, rather than depending on tympanic membranes like most land mammals. This arrangement does not give directional hearing under water.

Ambulocetus natans, which lived about 49 million years ago, was discovered in Pakistan in 1994. It was probably amphibious, and looked like a crocodile. In the Eocene, ambulocetids inhabited the bays and estuaries of the Tethys Ocean in northern Pakistan. The fossils of ambulocetids are always found in near-shore shallow marine deposits associated with abundant marine plant fossils and littoral molluscs. Although they are found only in marine deposits, their oxygen isotope values indicate that they consumed water with a range of degrees of salinity, some specimens showing no evidence of sea water consumption and others none of fresh water consumption at the time when their teeth were fossilized. It is clear that ambulocetids tolerated a wide range of salt concentrations. Their diet probably included land animals that approached water for drinking, or freshwater aquatic organisms that lived in the river. Hence, ambulocetids represent the transition phase of cetacean ancestors between freshwater and marine habitat.

Tiktaalik

Main articles: Tiktaalik and Evolution of tetrapods

Tiktaalik roseae had spiracles (air holes) above the eyes.

Life restoration of Tiktaalik roseae

Tiktaalik is a genus of extinct sarcopterygian (lobe-finned fish) from the Late Devonian period, with many features akin to those of tetrapods (four-legged animals). It is one of several lines of ancient sarcopterygians to develop adaptations to the oxygen-poor shallow water habitats of its time—adaptations that led to the evolution of tetrapods. Well-preserved fossils were found in 2004 on Ellesmere Island in Nunavut, Canada.

Tiktaalik lived approximately 375 million years ago. Paleontologists suggest that it is representative of the transition between non-tetrapod vertebrates such as Panderichthys, known from fossils 380 million years old, and early tetrapods such as Acanthostega and Ichthyostega, known from fossils about 365 million years old. Its mixture of primitive fish and derived tetrapod characteristics led one of its discoverers, Neil Shubin, to characterize Tiktaalik as a "fishapod." Unlike many previous, more fish-like transitional fossils, the "fins" of Tiktaalik have basic wrist bones and simple rays reminiscent of fingers. They may have been weight-bearing. Like all modern tetrapods, it had rib bones, a mobile neck with a separate pectoral girdle, and lungs, though it had the gills, scales, and fins of a fish. However in a 2008 paper by Boisvert at al. it is noted that Panderichthys, due to its more derived distal portion, might be closer to tetrapods than Tiktaalik, which might have independently developed similarities to tetrapods by convergent evolution.

Tetrapod footprints found in Poland and reported in Nature in January 2010 were "securely dated" at 10 million years older than the oldest known elpistostegids (of which Tiktaalik is an example), implying that animals like Tiktaalik, possessing features that evolved around 400 million years ago, were "late-surviving relics rather than direct transitional forms, and they highlight just how little we know of the earliest history of land vertebrates."

Amphistium

Main article: Flatfish § Evolution

Modern flatfish are asymmetrical, with both eyes on the same side of the head.

Fossil of Amphistium with one eye at the top-center of the head

Pleuronectiformes (flatfish) are an order of ray-finned fish. The most obvious characteristic of the modern flatfish is their asymmetry, with both eyes on the same side of the head in the adult fish. In some families the eyes are always on the right side of the body (dextral or right-eyed flatfish) and in others they are always on the left (sinistral or left-eyed flatfish). The primitive spiny turbots include equal numbers of right- and left-eyed individuals, and are generally less asymmetrical than the other families. Other distinguishing features of the order are the presence of protrusible eyes, another adaptation to living on the seabed (benthos), and the extension of the dorsal fin onto the head.

Amphistium is a 50-million-year-old fossil fish identified as an early relative of the flatfish, and as a transitional fossil. In Amphistium, the transition from the typical symmetric head of a vertebrate is incomplete, with one eye placed near the top-center of the head. Paleontologists concluded that "the change happened gradually, in a way consistent with evolution via natural selection—not suddenly, as researchers once had little choice but to believe."

Amphistium is among the many fossil fish species known from the Monte Bolca Lagerstätte of Lutetian Italy. Heteronectes is a related, and very similar fossil from slightly earlier strata of France.

Runcaria

The Devonian fossil plant Runcaria resembles a seed but lacks a solid seed coat and means to guide pollen.

Main articles: Runcaria and Evolution of plants § Seeds

A Middle Devonian precursor to seed plants has been identified from Belgium, predating the earliest seed plants by about 20 million years. Runcaria, small and radially symmetrical, is an integumented megasporangium surrounded by a cupule. The megasporangium bears an unopened distal extension protruding above the multilobed integument. It is suspected that the extension was involved in anemophilous pollination. Runcaria sheds new light on the sequence of character acquisition leading to the seed, having all the qualities of seed plants except for a solid seed coat and a system to guide the pollen to the seed.

Fossil record

See also: Taphonomy

Not every transitional form appears in the fossil record, because the fossil record is not complete. Organisms are only rarely preserved as fossils in the best of circumstances, and only a fraction of such fossils have been discovered. Paleontologist Donald Prothero noted that this is illustrated by the fact that the number of species known through the fossil record was less than 5% of the number of known living species, suggesting that the number of species known through fossils must be far less than 1% of all the species that have ever lived.

Because of the specialized and rare circumstances required for a biological structure to fossilize, logic dictates that known fossils represent only a small percentage of all life-forms that ever existed—and that each discovery represents only a snapshot of evolution. The transition itself can only be illustrated and corroborated by transitional fossils, which never demonstrate an exact half-way point between clearly divergent forms.

The fossil record is very uneven and, with few exceptions, is heavily slanted toward organisms with hard parts, leaving most groups of soft-bodied organisms with little to no fossil record. The groups considered to have a good fossil record, including a number of transitional fossils between traditional groups, are the vertebrates, the echinoderms, the brachiopods and some groups of arthropods.

History

See also: History of paleontology and Timeline of paleontology

Post-Darwin

Reconstruction of Rhynia

The idea that animal and plant species were not constant, but changed over time, was suggested as far back as the 18th century. Darwin's On the Origin of Species, published in 1859, gave it a firm scientific basis. A weakness of Darwin's work, however, was the lack of palaeontological evidence, as pointed out by Darwin himself. While it is easy to imagine natural selection producing the variation seen within genera and families, the transmutation between the higher categories was harder to imagine. The dramatic find of the London specimen of Archaeopteryx in 1861, only two years after the publication of Darwin's work, offered for the first time a link between the class of the highly derived birds, and that of the more basal reptiles. In a letter to Darwin, the palaeontologist Hugh Falconer wrote:

Had the Solnhofen quarries been commissioned—by august command—to turn out a strange being à la Darwin—it could not have executed the behest more handsomely—than in the Archaeopteryx.

Thus, transitional fossils like Archaeopteryx came to be seen as not only corroborating Darwin's theory, but as icons of evolution in their own right. For example, the Swedish encyclopedic dictionary Nordisk familjebok of 1904 showed an inaccurate Archaeopteryx reconstruction (see illustration) of the fossil, "ett af de betydelsefullaste paleontologiska fynd, som någonsin gjorts" ("one of the most significant paleontological discoveries ever made").

The rise of plants

Transitional fossils are not only those of animals. With the increasing mapping of the divisions of plants at the beginning of the 20th century, the search began for the ancestor of the vascular plants. In 1917, Robert Kidston and William Henry Lang found the remains of an extremely primitive plant in the Rhynie chert in Aberdeenshire, Scotland, and named it Rhynia.

The Rhynia plant was small and stick-like, with simple dichotomously branching stems without leaves, each tipped by a sporangium. The simple form echoes that of the sporophyte of mosses, and it has been shown that Rhynia had an alternation of generations, with a corresponding gametophyte in the form of crowded tufts of diminutive stems only a few millimetres in height. Rhynia thus falls midway between mosses and early vascular plants like ferns and clubmosses. From a carpet of moss-like gametophytes, the larger Rhynia sporophytes grew much like simple clubmosses, spreading by means of horizontal growing stems growing rhizoids that anchored the plant to the substrate. The unusual mix of moss-like and vascular traits and the extreme structural simplicity of the plant had huge implications for botanical understanding.

Missing links

"Java Man" or Pithecanthropus erectus (now Homo erectus), the original "missing link" found in Java in 1891–92

The human pedigree back to amoeba shown as a reinterpreted chain of being with living and fossil animals. From G. Avery's critique of Ernst Haeckel, 1873.

The idea of all living things being linked through some sort of transmutation process predates Darwin's theory of evolution. Jean-Baptiste Lamarck envisioned that life was generated constantly in the form of the simplest creatures, and strove towards complexity and perfection (i.e. humans) through a progressive series of lower forms. In his view, lower animals were simply newcomers on the evolutionary scene.

After On the Origin of Species, the idea of "lower animals" representing earlier stages in evolution lingered, as demonstrated in Ernst Haeckel's figure of the human pedigree. While the vertebrates were then seen as forming a sort of evolutionary sequence, the various classes were distinct, the undiscovered intermediate forms being called "missing links."

The term was first used in a scientific context by Charles Lyell in the third edition (1851) of his book Elements of Geology in relation to missing parts of the geological column, but it was popularized in its present meaning by its appearance on page xi of his book Geological Evidences of the Antiquity of Man of 1863. By that time, it was generally thought that the end of the last glacial period marked the first appearance of humanity; Lyell drew on new findings in his Antiquity of Man to put the origin of human beings much further back. Lyell wrote that it remained a profound mystery how the huge gulf between man and beast could be bridged. Lyell's vivid writing fired the public imagination, inspiring Jules Verne's Journey to the Center of the Earth (1864) and Louis Figuier's 1867 second edition of La Terre avant le déluge ("Earth before the Flood"), which included dramatic illustrations of savage men and women wearing animal skins and wielding stone axes, in place of the Garden of Eden shown in the 1863 edition.

The search for a fossil showing transitional traits between apes and humans, however, was fruitless until the young Dutch geologist Eugène Dubois found a skullcap, a molar and a femur on the banks of Solo River, Java in 1891. The find combined a low, ape-like skull roof with a brain estimated at around 1000 cc, midway between that of a chimpanzee and an adult human. The single molar was larger than any modern human tooth, but the femur was long and straight, with a knee angle showing that "Java Man" had walked upright. Given the name Pithecanthropus erectus ("erect ape-man"), it became the first in what is now a long list of human evolution fossils. At the time it was hailed by many as the "missing link," helping set the term as primarily used for human fossils, though it is sometimes used for other intermediates, like the dinosaur-bird intermediary Archaeopteryx.

Sudden jumps with apparent gaps in the fossil record have been used as evidence for punctuated equilibrium. Such jumps can be explained either by macromutation or simply by relatively rapid episodes of gradual evolution by natural selection, since a period of say 10,000 years barely registers in the fossil record.

While "missing link" is still a popular term, well-recognized by the public and often used in the popular media, the term is avoided in scientific publications. Some bloggers have called it "inappropriate"; both because the links are no longer "missing", and because human evolution is no longer believed to have occurred in terms of a single linear progression.

Punctuated equilibrium

Main article: Punctuated equilibrium

The theory of punctuated equilibrium developed by Stephen Jay Gould and Niles Eldredge and first presented in 1972 is often mistakenly drawn into the discussion of transitional fossils. This theory, however, pertains only to well-documented transitions within taxa or between closely related taxa over a geologically short period of time. These transitions, usually traceable in the same geological outcrop, often show small jumps in morphology between extended periods of morphological stability. To explain these jumps, Gould and Eldredge envisaged comparatively long periods of genetic stability separated by periods of rapid evolution. Gould made the following observation concerning creationist misuse of his work to deny the existence of transitional fossils:

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. The punctuations occur at the level of species; directional trends (on the staircase model) are rife at the higher level of transitions within major groups.

— Stephen Jay Gould, The Panda's Thumb