question: How is it possible that the extremely rare random mutations create enough similair new-type speciemen to start a new species?
comment: Luck has a large influence on survival as an individual and as a species. You might have a gene that lets you work sitting at a desk for several hours a day with out getting back pain or blood clots. But you have the bad luck of getting hit by a bus because your hearing isn't as good. Survival is about the aggregate good enough. Someone else might have a gene that gets blood clots in their 50s but has better hearing. Or just lucky they walked on the other side that day. It small changes that over the long haul make a new species, thousands of years in most cases.
passages: Perturbations can be genetic or epigenetic rather than environmental. For example, "Drosophila" fruit flies have a heat shock protein, Hsp90, which protects the development of many structures in the adult fly from heat shock. If the protein is damaged by a mutation, then just as if it were damaged by the environmental effects of drugs, many different phenotypic variants appear; if these are selected for, they quickly establish without further need for the mutant Hsp90.
  
  Section::::Neo-Darwinism or Lamarckism?
   The "Nup96" gene is another example of the evolution of the genes implicated in post-copulatory isolation. It regulates the production of one of the approximately 30 proteins required to form a nuclear pore. In each of the "simulans" groups of "Drosophila" the protein from this gene interacts with the protein from another, as yet undiscovered, gene on the X chromosome in order to form a functioning pore. However, in a hybrid the pore that is formed is defective and causes sterility. The differences in the sequences of "Nup96" have been subject to adaptive selection, similar to the other examples of "speciation genes" described above.
   BULLET::::- Mutations in germ-line DNA (i.e., DNA of the sperm or egg, which manifest in the offspring). These occur spontaneously, or are triggered by environmental radiation or mutagenic chemicals. A recently discovered mechanism, which is likely to be more important than the others combined, is infections with viruses, which integrate their DNA into their hosts. Organisms do not want to mutate: mutation just happens. Most of the mutations are harmful or lethal to the offspring, but a very small minority turn out to be advantageous, as novel proteins get produced that serve new functions.
   The first strain to become firmly established, and that which probably founded the present-day German Fallow, originated in Magdeburg, Germany, in 1932.
  
  The first two mutants were bred from a Cobalt cock and an Olive hen by Herr Schumann in May 1932, and this pair went on that year to produce seven more similar mutants in two further nests, giving a total of nine.
   In spirotrich ciliates (such as "Oxytricha"), the process is even more complex due to "gene scrambling": the MDSs in the micronucleus are often in different order and orientation from that in the macronuclear gene, and so in addition to deletion, DNA inversion and translocation are required for "unscrambling". This process is guided by long RNAs derived from the parental macronucleus. More than 95% of micronuclear DNA is eliminated during spirotrich macronuclear development.
  
  Section::::Fossil record.
   "New species arise by means of mass transformation of a great number of individuals, which happens due to Waagen mutations... This mass transformation is a phenomenon of geological magnitude. It is connected with the alteration of the fauna of a certain horizon and comes about in certain periods only to be absent for a long time"
   Few speciation genes have been found. They usually involve the reinforcement process of late stages of speciation. In 2008, a speciation gene causing reproductive isolation was reported. It causes hybrid sterility between related subspecies. The order of speciation of three groups from a common ancestor may be unclear or unknown; a collection of three such species is referred to as a "trichotomy."
  
  Section::::Genetics.:Speciation via polyploidy.
   The RIP mutations do not seem to be limited to repeated sequences. Indeed, for example, in the phytopathogenic fungus "L. maculans", RIP mutations are found in single copy regions, adjacent to the repeated elements. These regions are either non-coding regions or genes encoding small secreted proteins including avirulence genes.
  
  The degree of RIP within these single copy regions was proportional to their proximity to repetitive elements.
   Based on this Cab:luc fusion technology, Kay set up luciferase imaging assays for large scale forward genetics screening and identified the first short period mutant of TOC1 gene. TOC1 was proved to be a core clock gene in "Arabidopsis" and was cloned by Kay lab after a long period of time Kay also revealed the biochemical function of TOC1 and found that TOC1 and LHY/CCA1 reciprocally regulate each other, and further studied the mechanism of this regulation.
   Since "P. spyrothecae" clonally reproduce, genetic relatedness within colonies is rather simple: an individual aphid is either a clone of its neighbors or it is not. Since every generation within the gall displays a high degree of relatedness due to cloning, any deviation from a colony's genetic uniformity (excluding mutation) can be traced back to intergall migration. The ease of intergall migration is rooted in the fact that the colonies are present in the galls on the primary host for a long period of time, only migrating once the summer has passed.
   They then cultured two strains that chose opposite habitats. One of the strains emerged early, immediately flying upward in the dark attracted to the acetaldehyde. The other strain emerged late and immediately flew downward, attracted to light and ethanol. Pupae from the two strains were then placed together in the maze and allowed to mate at the food site. They then were collected. A selective penalty was imposed on the female flies that switched habitats. This entailed that none of their gametes would pass on to the next generation. After 25 generations of this mating test, it showed reproductive isolation between the two strains. They repeated the experiment again without creating the penalty against habitat switching and the result was the same; reproductive isolation was produced.
   BULLET::::- Star Ruby and Rio red varieties of the Rio Star Grapefruit (created using thermal neutron techniques)
  
  BULLET::::- Todd's Mitcham Peppermint ("Verticillium" wilt tolerance)
  
  BULLET::::- VND 95-20, VND-99-1 and VN121 rice mutants (increased yield, improved quality, resistance to disease and pests)
  
  BULLET::::- DT84, DT96, DT99 and DT 2008 soybean mutants (developed using gamma rays to grow three crops a year, tolerance to heat and cold and resistance to disease)
   The second chapter argues that mutations occur frequently and are random in direction. Most are small in effect, but they affect all features of organisms and vary from beneficial to lethal. They are sufficient to provide the raw material for natural selection.
  
  Section::::Contents of the first edition.:Mutation as a basis for racial and specific differences.
  
  In the third chapter, Dobzhansky demonstrates that the mutations that are observed in the laboratory also occur in nature, where they are acted on by natural selection. Thus, there is nothing intrinsically different about the process by which new species evolve.
   Section::::Rate of transposition, induction and defense.
  
  One study estimated the rate of transposition of a particular retrotransposon, the Ty1 element in "Saccharomyces cerevisiae". Using several assumptions, the rate of successful transposition event per single Ty1 element came out to be about once every few months to once every few years. Some TEs contain heat-shock like promoters and their rate of transposition increases if the cell is subjected to stress, thus increasing the mutation rate under these conditions, which might be beneficial to the cell.
   Section::::New mutagen techniques.:Ion beam technology.
   The first RNAi screen (based on DNA FISH) was carried out to identify genes regulating "D. melanogaster" somatic pairing in 2012, described at the time as providing "an extensive “parts list” of mostly novel factors". These comprised 40 pairing promoting genes and 65 'anti-pairing' genes (of which 2 and 1 were already known, respectively), many of which have human orthologs.
   Evolution of novel polyphenisms through this mechanism has been demonstrated in the laboratory. Suzuki and Nijhout used an existing mutation ("black") in a monophenic green hornworm ("Manduca sexta") that causes a black phenotype. They found that if larvae from an existing population of "black" mutants were raised at 20˚C, then all the final instar larvae were black; but if the larvae were instead raised at 28˚C, the final instar larvae ranged in color from black to green. By selecting for larvae that were black if raised at 20˚C but green if raised at 28˚C, they produced a polyphenic strain after thirteen generations.
   BULLET::::1. taking into account the upper size limit to most microsatellites
  
  BULLET::::2. factoring in the likelihood of large alleles to show higher rates of mutation than small alleles
  
  BULLET::::3. and including variations that suggest that mutations are split between point mutations that disrupt stretches of repeats and the additions or removal of repeat units. This last assumption provides an explanation for why microsatellites do not evolve into enormous arrays of infinite size.
   The "D. melanogaster" lineage is illustrative of these differing approaches. An early survey using a combination of BLAST searches performed on cDNA sequences along with manual searches and synteny information identified 72 new genes specific to "D. melanogaster" and 59 new genes specific to three of the four species in the "D. melanogaster" species complex. This report found that only 2/72 (~2.8%) of "D. melanogaster"-specific new genes and 7/59 (~11.9%) of new genes specific to the species complex were derived "de novo", with the remainder arising via duplication/retroposition. Similarly, an analysis of 195 young (<35 million years old) "D. melanogaster" genes identified from syntenic alignments found that only 16 had arisen "de novo". In contrast, an analysis focused on transcriptomic data from the testes of six "D. melanogaster" strains identified 106 fixed and 142 segregating "de novo" genes. For many of these, ancestral ORFs were identified but were not expressed. Highlighting the differences between inter- and intra-species comparisons, a study in natural "Saccharomyces paradoxus" populations found that the number of de novo polypeptides identified more than doubled when considering intra-species diversity. In primates, one early study identified 270 orphan genes (unique to humans, chimpanzees, and macaques), of which 15 were thought to have originated "de novo", while a later report identified 60 "de novo" genes in humans alone that are supported by transcriptional and proteomic evidence. Studies in other lineages/organisms have also reached different conclusions with respect to the number of de novo genes present in each organism, as well as the specific sets of genes identified. A sample of these large-scale studies is described in the table below.
   BULLET::::2. Random transposition occurs, inserting the reporter gene randomly. The insertion tends to occur near actively transcribed genes, as this is where the chromatin structure is loosest, so the DNA is most accessible.
  
  BULLET::::3. Grow flies and cross to remove genetic variation between the cells of the organism (see above).
  
  BULLET::::4. Look for flies expressing the reporter gene. These have experienced a successful transposition, so can be investigated to determine the phenotype due to mutation of existing genes.
  
  "Possible mutations:"
   The Dobzhansky-Muller model proposes that reproductive incompatibilities between species are caused by the interaction of the genes of the respective species. It has been demonstrated recently that "Lhr" has functionally diverged in "D. simulans" and will interact with "Hmr" which, in turn, has functionally diverged in "D. melanogaster" to cause the lethality of the male hybrids. "Lhr" is located in a heterochromatic region of the genome and its sequence has diverged between these two species in a manner consistent with the mechanisms of positive selection. An important unanswered question is whether the genes detected correspond to old genes that initiated the speciation favoring hybrid non-viability, or are modern genes that have appeared post-speciation by mutation, that are not shared by the different populations and that suppress the effect of the primitive non-viability genes. The "OdsH" (abbreviation of "Odysseus") gene causes partial sterility in the hybrid between "Drosophila simulans" and a related species, "D. mauritiana", which is only encountered on Mauritius, and is of recent origin. This gene shows monophyly in both species and also has been subject to natural selection. It is thought that it is a gene that intervenes in the initial stages of speciation, while other genes that differentiate the two species show polyphyly. "Odsh" originated by duplication in the genome of "Drosophila" and has evolved at very high rates in "D. mauritania", while its paralogue, "unc-4", is nearly identical between the species of the group "melanogaster". Seemingly, all these cases illustrate the manner in which speciation mechanisms originated in nature, therefore they are collectively known as "speciation genes", or possibly, gene sequences with a normal function within the populations of a species that diverge rapidly in response to positive selection thereby forming reproductive isolation barriers with other species. In general, all these genes have functions in the transcriptional regulation of other genes.
   In 2006 and 2007, a series of studies provided arguably the first documented examples of "de novo" gene birth that did not involve overprinting. An analysis of the accessory gland transcriptomes of "Drosophila yakuba" and "Drosophila erecta" first identified 20 putative lineage-restricted genes that appeared unlikely to have resulted from gene duplication. Levine and colleagues then confirmed the "de novo" origination of five candidate genes specific to "Drosophila melanogaster" and/or the closely related "Drosophila simulans" through a rigorous pipeline that combined bioinformatic and experimental techniques. These genes were identified by combining BLAST search-based and synteny-based approaches (see below), which demonstrated the absence of the genes in closely-related species.
   Gall and then-graduate student Mary-Lou Pardue wanted to find out where in the chromosomes a distinctive highly repeated DNA sequence called satellite DNA occurred. To show the location of this special DNA, they developed the widely used laboratory technique known as "in situ hybridization". Using this method, they found that satellite DNA occurred at the ends or telomeres of the chromosomes.
   Other hybrids descended from the same two parents are known. Some are infertile, such as "S." x "baxteri". Other fertile hybrids are also known, including "S. vulgaris" var. "hibernicus", now common in Britain, and the allohexaploid "S. cambrensis", which according to molecular evidence probably originated independently at least three times in different locations. Morphological and genetic evidence support the status of "S. eboracensis" as separate from other known hybrids.
  
  Section::::Evidence from speciation.:Plants.:Thale cress.
   In an additional study, the researchers studied two gall wasp species "B. treatae" and "Disholcaspis quercusvirens" and found strong morphological and behavioral variation among host-associated populations. This study further confounded prerequisites to speciation.
  
  Section::::Evidence from speciation.:Invertebrates.:Hawthorn fly.
  
raw_presuppositions: Extremely rare mutations are too rare to create a new species. Extremely rare random mutations create a large number of variations to start a new species. 
raw_corrections: Given enough time and luck, small mutations can create a new species. Extremely rare random mutations create small variations aggregated over thousands of years in order to start a new species.