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

Adaptive mutation

From Wikipedia, the free encyclopedia

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

Adaptive mutation, also called directed mutation or directed mutagenesis is a controversial evolutionary theory. It posits that mutations, or genetic changes, are much less random and more purposeful than traditional evolution, implying that organisms can respond to environmental stresses by directing mutations to certain genes or areas of the genome. There have been a wide variety of experiments trying to support (or disprove) the idea of adaptive mutation, at least in microorganisms.

Definition

The most widely accepted theory of evolution states that organisms are modified by natural selection where changes caused by mutations improve their chance of reproductive success. Adaptive mutation states that rather than mutations and evolution being random, they are in response to specific stresses. In other words, the mutations that occur are more beneficial and specific to the given stress, instead of random and not a response to anything in particular. The term stress refers to any change in the environment, such as temperature, nutrients, population size, etc. Tests with microorganisms have found that for adaptive mutation, more of the mutations observed after a given stress were more effective at dealing with the stress than chance alone would suggest is possible. This theory of adaptive mutation was first brought to academic attention in the 1980s by John Cairns.

Recent studies

Adaptive mutation is a controversial claim leading to a series of experiments designed to test the idea. Three major experiments are the SOS response, responses to starvation in Escherichia coli, and testing for revertants of a tryptophan auxotroph in Saccharomyces cerevisiae (yeast).

Lactose starvation

The E. coli strain FC40 has a high rate of mutation, and so is useful for studies, such as for adaptive mutation. Due to a frameshift mutation, a change in the sequence that causes the DNA to code for something different, FC40 is unable to process lactose. When placed in a lactose-rich medium, it has been found that 20% of the cells mutated from Lac- (could not process lactose) to Lac+, meaning they could now utilize the lactose in their environment. The responses to stress are not in current DNA, but the change is made during DNA replication through recombination and the replication process itself, meaning that the adaptive mutation occurs in the current bacteria and will be inherited by the next generations because the mutation becomes part of the genetic code in the bacteria. This is particularly obvious in a study by Cairns, which demonstrated that even after moving E. coli back to a medium with minimal levels of lactose, Lac+ mutants continued to be produced as a response to the previous environment. This would not be possible if adaptive mutation was not at work because natural selection would not favor this mutation in the new environment. Although there are many genes involved in adaptive mutation, RecG, a protein, was found to have an effect on adaptive mutation. By itself, RecG was found to not necessarily lead to a mutational phenotype. However, it was found to inhibit the appearance of revertants (cells that appeared normally, as opposed to those with the mutations being studied) in wild type cells. On the other hand, RecG mutants were key to the expression of RecA-dependent mutations, which were a major portion of study in the SOS response experiments, such as the ability to utilize lactose.

Adaptive mutation was re-proposed in 1988 by John Cairns who was studying Escherichia coli that lacked the ability to metabolize lactose. He grew these bacteria in media in which lactose was the only source of energy. In doing so, he found that the rate at which the bacteria evolved the ability to metabolize lactose was many orders of magnitude higher than would be expected if the mutations were truly random. This inspired him to propose that the mutations that had occurred had been directed at those genes involved in lactose utilization.

Later support for this hypothesis came from Susan Rosenberg, then at the University of Alberta, who found that an enzyme involved in DNA recombinational repair, recBCD, was necessary for the directed mutagenesis observed by Cairns and colleagues in 1989. The directed mutagenesis hypothesis was challenged in 2002, by work showing that the phenomenon was due to general hypermutability due to selected gene amplification, followed by natural selection, and was thus a standard Darwinian process. Later research from 2007 however, concluded that amplification could not account for the adaptive mutation and that "mutants that appear during the first few days of lactose selection are true revertants that arise in a single step".

SOS response

This experiment is different from the others in one small way: this experiment is concerned with the pathways leading to an adaptive mutation while the others tested the changing environment microorganisms were exposed to. The SOS response in E. coli is a response to DNA damage that must be repaired. The normal cell cycle is put on hold and mutagenesis may begin. This means that mutations will occur to try to fix the damage. This hypermutation, or increased rate of change, response has to have some regulatory process, and some key molecules in this process are RecA, and LexA. These are proteins and act as stoplights for this and other processes. They also appear to be the main contributors to adaptive mutation in E. coli. Changes in presence of one or the other was shown to affect the SOS response, which in turn affected how the cells were able to process lactose, which should not be confused with the lactose starvation experiment. The key point to understand here is that LexA and RecA both were required for adaptive mutation to occur, and without the SOS response adaptive mutation would not be possible.

Yeast

von Borstel, in the 1970s, conducted experiments similar to the Lactose Starvation experiment with yeast, specifically Saccharomyces cerevisiae. He tested for tryptophan auxotroph revertants. A tryptophan auxotroph cannot make tryptophan for itself, but wild-type cells can and so a revertant will revert to the normal state of being able to produce tryptophan. He found that when yeast colonies were moved from a tryptophan-rich medium to a minimal one, revertants continued to appear for several days. The degree to which revertants were observed in yeast was not as high as with bacteria. Other scientists have conducted similar experiments, such as Hall who tested histidine revertants, or Steele and Jinks-Robertson who tested lysine. These experiments demonstrate how recombination and DNA replication are necessary for adaptive mutation. However, in lysine-tested cells, recombination continued to occur even without selection for it. Steele and Jinks-Robertson concluded that recombination occurred in all circumstances, adaptive or otherwise, while mutations were present only when they were beneficial and adaptive.

Although the production of mutations during selection was not as vigorous as observed with bacteria, these studies are convincing. As mentioned above, a subsequent study adds even more weight to the results with lys2. Steele and Jinks-Robertson found that LYS prototrophs due to interchromosomal recombination events also continue to arise in nondividing cells, but in this case, the production of recombinants continued whether there was selection for them or not. Thus, mutation occurred in stationary phase only when it was adaptive, but recombination occurred whether it was adaptive or not.

Delayed appearance of mutants has also been reported for Candida albicans. With long exposure to sublethal concentrations of heavy metals, colonies of resistant cells began to appear after 5–10 days and continued to appear for 1–2 weeks thereafter. These resistances could have resulted from gene amplification, although the phenotypes were stable during a short period of nonselective growth. However, revertants of two auxotrophies also appeared with similar kinetics. None of these events in Candida albicans have, as yet, been shown to be specific to the selection imposed.

Ecological-evolutionary theory

From Wikipedia, the free encyclopedia

 https://en.wikipedia.org/wiki/Ecological-evolutionary_theory

Ecological-evolutionary theory (EET) is a sociological theory of sociocultural evolution that attempts to explain the origin and changes of society and culture. Key elements focus on the importance of natural environment and technological change. EET has been described as a theory of social stratification, as it analyzes how stratification has changed through time across different societies. It also has been viewed as a synthesis of the structural functionalism and conflict theory. Proposed by Gerhard Lenski, the theory perhaps is best articulated in his book, Ecological-Evolutionary Theory: Principles and Applications (2005). His major collaborators, Jean Lenski and Patrick Nolan, also are said to have contributed to EET.

Theory

Lenski notes that society and culture evolve through symbols, which makes this process much more rapid, deliberative, and purposeful, compared to biological evolution. However, just like in the biological survival of the fittest, in sociocultural evolution there is a process of intersocietal selection, where less fit sociocultural systems became extinct, replaced by more efficient ones. In another analogy to biological evolution, Lenski argues that the sociocultural systems that survive do so primarily on the virtue of their level of technological advancement, which otherwise is "blind and purposeless as the outcome of the biological process of natural selection and just as indifferent to humans beliefs and values". Thus, Lenski does not argue that societies that survive are morally superior to those that are defeated—simply that they were more efficient at technological progress. This, in turn, helps those societies survive and grow. Technologies can thus be compared to genes of a society, providing it with new abilities, as new technologies allow it to do things that it could not have done before.

Technology is a factor whose importance Lenski stresses above all others, and he differentiates societies by their technology level, into hunter gatherers, simple and complex horticulture, agrarian societies and industrial societies. At the same time, characteristics of a society go beyond technology, into its demographic and genetic characteristics; culture, including material; social organization and institutions. Natural environment also plays a role, as does geographical location in general; as isolated societies have less chance to benefit from interaction with others.

Lenski's theory focus on material infrastructure of societies (growth in population and economic relations), and as such has been described as materialist. It builds on classic theories of Thomas Malthus and Herbert Spencer in seeing society and culture as products of nature (human beings), thus subject to natural law. Lenski argues that humans often act against the interests of the society, which he attributes to self-interest and individualism, themselves products of differing life experiences. He notes that different societies survive thanks to their subsistence strategies, which allow them to draw resources (energy) from the environment; those strategies are determined by technologies possessed by those societies, itself significantly determined by demography (population and its growth) and economy systems (division of labor). Technology, defined by him as "information about the ways in which resources in the environment may be used to satisfy human needs and desires," is the most important element of the sociocultural system.

Lenski further argues that sociocultural change is an effect of either interaction with a different society and culture, or a result of environment change (from natural ones, like ice ages, to man-made ones, like resource depletion). Humans primary way of dealing with changing environment is a self-reinforcing development of technology, through innovation is in general less common than copying solutions invented by others (cultural diffusion).

All societies share two partially competing goals: maximization of production and minimizing of political change (maintenance of powers by the elites). The higher the social stratification, the more dominant the second goal is. Lenski theory can be thus used to analyze the changes of social inequality. Lenski notes that some level of social inequality is expected in all societies, as it is related to differences in abilities of individuals and the tasks they chose to perform for the society; but he also observes that inequality in all societies has always been higher than ideal, as elites usually try to preserve their dominant status. Lenski argues that inequality reached its peak levels in agrarian societies or industrial ones, and have been slowly declining since.

Lenski observes that the forces of technological change (innovation) are in constant conflict with forces of continuity and stability, such as traditions, conservatism, opposition of vested interests to disruptive technologies, and general tendency of humans to resist change. He concludes, however, that usually technological progress overcomes any obstacles, forcing sociocultural systems to change. Lenski also observes that technological change accelerates over time.

The theory has been praised as "a synthesis of key insights of the founders of sociology and of contemporary macrosociology and anthropology".