In cases of  co-dominance , the genetic traits of both different alleles of the same gene-locus are clearly  expressed  in the phenotype. For example, in certain varieties of chicken, the allele for black feathers is co-dominant with the allele for white feathers. Heterozygous chickens have a colour described as "erminette", speckled with black and white feathers appearing separately. Many human genes, including one for a protein that controls cholesterol levels in the blood, show co-dominance too. People with the heterozygous form of this gene produce two different forms of the protein, each with a different effect on cholesterol levels. [ citation needed ]


When genes are located on the same chromosome and no  crossing over  took place before the segregation of the chromosomes into the  gametes , the  genetic traits  will be inherited in connection, because of the  genetic linkage . These cases constitute an exception to the Mendelian rule of independent assortment. [ citation needed ]


In Mendelian inheritance, genes have only two alleles, such as  a  and  A . Mendel consciously chose pairs of genetic traits, represented by two alleles for his inheritance experiments. In nature, such genes often exist in several different forms and are therefore said to have  multiple alleles . An individual usually has only two copies of each gene, but many different alleles are often found within a population. A rabbit's coat color is determined by a single gene that has at least four different alleles. They display a pattern of a dominance-hierarchy that can produce four coat colors. In the genes for the  dog coat colours  there are four alleles on the Agouti-locus. The allele "aw" is dominant over the alleles "at" and "a" but recessive under "Ay". [ citation needed ]


Many other genes have multiple alleles, including the human genes for  ABO blood type . [ citation needed ]


If one or more genes cannot be expressed because of another genetic factor hindering their expression, this  epistasis  can make it impossible even for dominant alleles on certain other gene-loci to have an effect on the phenotype. An example in  dog coat genetics  is the homozygosity with the allele "e e" on the Extension-locus making it impossible to produce any other pigment than pheomelanin. Although the allele "e" is a recessive allele on the extension-locus itself, the presence of two copies leverages the dominance of other coat colour genes. Domestic cats have a gene with a similar effect on the X-chromosome. [ citation needed ]


Genetic traits located on  gonosomes  sometimes show specific non-Mendelian inheritance patterns. Individuals can develop a recessive trait in the phenotype dependent on their sex—for example,  colour blindness  and  haemophilia  (see  gonosomal inheritances ). [ 7 ] [ 8 ]  As many of the alleles are dominant or recessive, a true understanding of the principles of  Mendelian inheritance  is an important requirement to also understand the more complicated inheritance patterns of sex-linked inheritances. [ citation needed ]


Extranuclear inheritance  (also known as cytoplasmic inheritance) is a form of non-Mendelian inheritance also first discovered by Carl Correns in 1908. [ 9 ]  While working with  Mirabilis jalapa ,  Correns observed that leaf colour was dependent only on the genotype of the maternal parent.  Based on these data, he determined that the trait was transmitted through a character present in the  cytoplasm  of the  ovule . Later research by  Ruth Sager  and others identified DNA present in  chloroplasts  as being responsible for the unusual inheritance pattern observed. Work on the poky strain of the mould  Neurospora crassa  begun by Mary and  Hershel Mitchell [ 10 ]  ultimately led to the discovery of genetic material in the mitochondria, the  mitochondrial DNA . [ citation needed ]


According to the  endosymbiont  theory, mitochondria and chloroplasts were once free-living organisms that were each taken up by a eukaryotic cell. [ 11 ]  Over time, mitochondria and chloroplasts formed a  symbiotic  relationship with their eukaryotic hosts. Although the transfer of a number of genes from these organelles to the nucleus prevents them from living independently, each still possesses genetic material in the form of double stranded DNA. [ citation needed ]


It is the transmission of this  organellar  DNA that is responsible for the phenomenon of extranuclear inheritance. Both chloroplasts and mitochondria are present in the cytoplasm of maternal gametes only. Paternal gametes ( sperm  for example) do not have cytoplasmic mitochondria [ citation needed ] .  Thus, the  phenotype  of traits linked to genes found in either chloroplasts or mitochondria are determined exclusively by the maternal parent.


In humans,  mitochondrial diseases  are a class of diseases, many of which affect the muscles and the eye. [ citation needed ]


Many traits are produced by the interaction of several genes. Traits controlled by two or more genes are said to be  polygenic traits .  Polygenic  means "many genes" are necessary for the organism to develop the trait. For example, at least three genes are involved in making the reddish-brown pigment in the eyes of  fruit flies . Polygenic traits often show a wide range of phenotypes. The broad variety of  skin colour in humans  comes about partly because at least four different genes probably control this trait. [ citation needed ]


Non-random segregation of chromosomes  is a deviation from the usual distribution of chromosomes during meiosis and in some cases of mitosis.


Gene conversion  can be one of the major forms of non-Mendelian inheritance. Gene conversion arises during DNA repair via DNA  recombination , by which a piece of DNA sequence information is transferred from one DNA helix (which remains unchanged) to another DNA helix, whose sequence is altered. This may occur as a  mismatch repair  between the strands of DNA which are derived from different parents. Thus the mismatch repair can convert one  allele  into the other. This phenomenon can be detected through the offspring non-Mendelian ratios, and is frequently observed, e.g., in fungal crosses. [ 12 ]


Another form of non-Mendelian inheritance is known as infectious heredity. Infectious particles such as  viruses  may infect host cells and continue to reside in the cytoplasm of these cells. If the presence of these particles results in an altered phenotype, then this phenotype may be subsequently transmitted to progeny. [ 13 ]  Because this phenotype is dependent only on the presence of the invader in the host cell's cytoplasm, inheritance will be determined only by the infected status of the maternal parent. This will result in a uniparental transmission of the trait, just as in extranuclear inheritance. [ citation needed ]


One of the most well-studied examples of infectious heredity is the killer phenomenon exhibited in  yeast . Two double-stranded  RNA viruses , designated L and M, are responsible for this phenotype. [ 14 ]  The L virus codes for the  capsid  proteins of both viruses, as well as an  RNA polymerase . Thus the M virus can only infect cells already harbouring L virus particles. The M viral RNA encodes a  toxin  that is secreted from the host cell. It kills susceptible cells growing in close proximity to the host.  The M viral RNA also renders the host cell immune to the lethal effects of the toxin. For a cell to be susceptible it must therefore be either uninfected or harbour only the L virus. [ citation needed ]


The L and M viruses are not capable of exiting their host cell through conventional means. They can only transfer from cell to cell when their host undergoes mating. All progeny of a mating involving a doubly infected yeast cell will also be infected with the L and M viruses. Therefore, the killer phenotype will be passed down to all progeny. [ citation needed ]


Heritable traits that result from infection with foreign particles have also been identified in  Drosophila . Wild-type flies normally fully recover after being anesthetized with carbon dioxide.  Certain lines of flies have been identified that die off after exposure to the compound. This carbon dioxide sensitivity is passed down from mothers to their progeny. This sensitivity is due to infection with σ (Sigma) virus, a  rhabdovirus  only capable of infecting  Drosophila . [ 15 ]


Although this process is usually associated with viruses, recent research has shown that the  Wolbachia  bacterium is also capable of inserting its genome into that of its host. [ 16 ] [ 17 ]


Genomic imprinting represents yet another example of non-Mendelian inheritance. Just as in conventional inheritance, genes for a given trait are passed down to progeny from both parents. However, these genes are  epigenetically  marked before transmission, altering their levels of expression. These imprints are created before gamete formation and are erased during the creation of germ line cells. Therefore, a new pattern of imprinting can be made with each generation. [ citation needed ]


Genes are imprinted differently depending on the parental origin of the  chromosome  that contains them. In mice, the  insulin-like growth factor 2  gene undergoes imprinting. The  protein  encoded by this gene helps to regulate body size. Mice that possess two functional copies of this gene are larger than those with two mutant copies. The size of mice that are heterozygous at this locus depends on the parent from which the wild-type  allele  came. If the functional allele originated from the mother, the offspring will exhibit  dwarfism , whereas a paternal allele will generate a normal-sized mouse.  This is because the maternal  Igf2  gene is imprinted. Imprinting results in the inactivation of the  Igf2  gene on the chromosome passed down by the mother. [ 18 ]


Imprints are formed due to the differential  methylation  of paternal and maternal alleles. This results in differing expression between alleles from the two parents. Sites with significant methylation are associated with low levels of  gene expression . Higher gene expression is found at unmethylated sites. [ 19 ]  In this mode of inheritance, phenotype is determined not only by the specific allele transmitted to the offspring, but also by the sex of the parent that transmitted it.


Individuals who possess cells with genetic differences from the other cells in their body are termed mosaics. These differences can result from  mutations  that occur in different tissues and at different periods of development. If a mutation happens in the non-gamete forming tissues, it is characterized as  somatic .  Germline  mutations occur in the egg or sperm cells and can be passed on to offspring. [ 20 ]  Mutations that occur early on in development will affect a greater number of cells and can result in an individual that can be identified as a mosaic strictly based on phenotype.


Mosaicism  also results from a phenomenon known as  X-inactivation . All female mammals have two  X chromosomes . To prevent lethal  gene dosage  problems, one of these chromosomes is inactivated following  fertilization . This process occurs randomly for all of the cells in the organism's body. Because a given female's two X chromosomes will almost certainly differ in their specific pattern of alleles, this will result in differing cell phenotypes depending on which chromosome is silenced.  Calico cats , which are almost all female, [ 21 ]  demonstrate one of the most commonly observed manifestations of this process. [ 22 ]


Trinucleotide repeat disorders also follow a non-Mendelian pattern of inheritance.  These diseases are all caused by the expansion of  microsatellite   tandem repeats  consisting of a stretch of three  nucleotides . [ 23 ]   Typically in individuals, the number of repeated units is relatively low.  With each successive generation, there is a chance that the number of repeats will expand.  As this occurs, progeny can progress to premutation and ultimately affected status.  Individuals with a number of repeats that falls in the premutation range have a good chance of having affected children.  Those who progress to affected status will exhibit symptoms of their particular disease.  Prominent trinucleotide repeat disorders include  Fragile X syndrome  and  Huntington's disease .  In the case of Fragile X syndrome it is thought that the symptoms result from the increased methylation and accompanying reduced expression of the fragile X intellectual disability gene in individuals with a sufficient number of repeats. [ 24 ]


A  null allele  is a nonfunctional  allele  (a variant of a  gene ) caused by a genetic  mutation . Such mutations can cause a complete lack of production of the associated  gene product  or a product that does not function properly; in either case, the allele may be considered nonfunctional. A null allele cannot be distinguished from  deletion  of the entire  locus  solely from  phenotypic  observation. [ 1 ]


A mutant allele that produces no  RNA  transcript is called an  RNA null  (shown by  Northern blotting  or by  DNA sequencing  of a deletion allele), and one that produces no  protein  is called a  protein null  (shown by  Western blotting ). A  genetic null  or  amorphic  allele has the same phenotype when  homozygous  as when  heterozygous  with a deficiency that disrupts the locus in question. A genetic null allele may be both a protein null and an RNA null, but may also express normal levels of a gene product that is nonfunctional due to mutation.


Null alleles can have lethal effects depending on the importance of the mutated gene. For example, mice homozygous for a null allele for  insulin  die 48 to 72 hours after birth. [ 2 ]  Null alleles can also have beneficial effects, [ 3 ]  such as the elevated harvest index of semi-dwarf rice of the  green revolution  caused by null alleles in GA20ox-2.  [ 4 ]


A microsatellite null allele is an allele at a  microsatellite  locus that does not amplify to detectable levels in a  polymerase chain reaction  test. [ 5 ]  Microsatellite regions are usually characterized by short, repeated sequences of nucleotides. [ 5 ]   Primers  that are specific to a particular locus are used in PCR amplification to bind to these nucleotide sequence repeats and are used as genetic markers. [ 6 ] [ 5 ]  The primers anneal to either end of the locus and are derived from source organisms in a genomic library. Divergence from the reference sequences (from genetic mutations) results in poor annealing of the primers so that the marker cannot be used, representative of a null allele. [ 6 ]


Strong evidence of null alleles was first seen in analysis of bears in 1995. [ 7 ]  In this analysis, a known parent was determined to be homozygous at a certain locus, but produced offspring that expressed a different "homozygous" genotype. [ 5 ]  This result led to the inference that the parent and offspring were both heterozygous for the locus being studied. [ 7 ]


Null alleles or genes have been studied in different organisms from the red pines of Minnesota to  Drosophila melanogaster  and mice. Null alleles are difficult to identify because a heterozygous individual for one null allele and one active allele is phenotypically indistinguishable from a homozygous individual with both active alleles. [ 8 ]  In other words, a null allele can only be identified from the phenotypic standpoint if the individual is homozygous for the null allele. Researchers have been able to work around this problem by using detailed  Electrophoresis , gel assays, and chromosomal manipulation. [ 8 ] [ 9 ] [ 10 ]


The  ob/ob  or  obese  mouse  is a  mutant  mouse that  eats excessively  due to mutations in the gene responsible for the production of  leptin  and becomes profoundly  obese . It is an  animal model  of  type II diabetes . Identification of the  gene  mutated in  ob  led to the discovery of the  hormone  leptin, which is important in the control of appetite.


The first  ob/ob  mouse arose by chance in a colony at the  Jackson Laboratory  in 1949. [ 1 ]  The mutation is  recessive . Mutant mice are phenotypically indistinguishable from their unaffected littermates at birth, but gain weight rapidly throughout their lives, reaching a weight three times that of unaffected mice.  ob/ob  mice develop  high blood sugar , despite an  enlargement  of the  pancreatic islets  and  increased levels of insulin . [ 2 ]


The gene affected by the  ob  mutation was identified by  positional cloning . [ 3 ]  The gene produces a hormone, called leptin, that is produced predominantly in  adipose tissue . One role of leptin is to regulate appetite by signalling to the brain that the animal has had enough to eat. [ 4 ]  Since the  ob/ob  mouse cannot produce leptin, its food intake is uncontrolled by this mechanism.


A positional cloning approach in the Lep ob  mouse allows to identify the locus of the gene encoding for the ob protein. Clones were used to construct a contig across most of the 650-kb critical region of ob. Exons from this interval were trapped using exon trapping method and each was afterward sequenced and searched in the  GenBank . One of the exons was hybridized to a Northern blot of mouse white adipose tissue (WAT). This allowed to investigate the levels of ob gene expression which seemed to be markedly increased in WAT of Lep ob  mice. This is consistent with a biologically inactive truncated protein. [ 3 ]


Oligogenic inheritance  ( Greek  ὀλίγος –  ὀligos  = few, a little) describes a trait that is influenced by a few genes. Oligogenic inheritance represents an intermediate between  monogenic inheritance  in which a trait is determined by a single causative gene, and  polygenic inheritance , in which a trait is influenced by many genes and often environmental factors. [ 1 ]


Historically, many traits were thought to be governed by a single causative gene (in what is deemed  monogenic inheritance ), however work in genetics revealed that these traits are comparatively rare, and in most cases so-called monogenic traits are predominantly influenced by one gene, but can be mediated by other genes of small effect. [ 2 ]


Around the 1930s/40s, evidence that multiple genes could affect the risk of disease that showed discrete inheritance patterns, due to differences in the age of onset of disease for siblings. The age of onset for sibling pairs was very similar, but between pairs of siblings could be quite different, and would in some cases cluster into several age brackets. This suggested a major gene that controlled the risk for a disease, and other genes that impacted age of onset. [ 3 ]


The recognition of diseases which were influenced by more than one gene highlighted a need to develop methodologies for detecting these oligogenic inheritance patterns, as they did not fit the more straightforward Mendelian model of inheritance. The developments of such methods accelerated the discovery of other examples of oligogenic traits, and sparked a change in the way genetic disease was perceived. [ 1 ]


One example of oligogenic inheritance is a case where one gene is sufficient to cause a trait, however its  penetrance  or  expressivity  is influenced by another gene, called a modifier. An example of such a case is the gene  TGFB1  which modified a person's risk of developing Alzheimer's disease if they are carrying the disease variant of the gene  APP . The mechanism is thought to work through the modifier variant increasing the clearance of amyloid fibers in the aging brain, reducing plaque burden. [ 4 ]


A trait can be recognised as oligogenic through the following lines of evidence: [ 1 ]


Overdominance  is a phenomenon in genetics where the  phenotype  of the  heterozygote  lies outside the phenotypical range of both  homozygous  parents. Overdominance can also be described as  heterozygote advantage  regulated by a single  genomic   locus , wherein  heterozygous  individuals have a higher  fitness  than  homozygous  individuals. However, not all cases of the heterozygote advantage are considered overdominance, as they may be regulated by multiple genomic regions. [ 1 ]  Overdominance has been hypothesized as an underlying cause for  heterosis  (increased fitness of hybrid offspring). [ 2 ] [ 3 ]


An example of overdominance in humans is that of the  sickle cell anemia . This condition is determined by a single  polymorphism . Possessors of the deleterious allele have lower life expectancy, with  homozygotes  rarely reaching 50 years of age. However, this allele also yields some resistance to  malaria . Thus in regions where malaria exerts or has exerted a strong selective pressure, sickle cell anemia has been selected for its conferred partial resistance to the disease. While homozygotes will have either no protection from malaria or a dramatic propensity to sickle cell anemia,  heterozygotes  have fewer physiological effects and a partial resistance to malaria. [ 4 ]


Major histocompatibility complex  (MHC) genes exhibit extensive variation, generally attributed to the notion of heterozygous individuals identifying a wider range of peptides than homozygous individuals. In  arctic char  population in  Finland , fish heterozygous for MHC alleles had fewer cysts, grew larger, and had a better chance at survival, all indicating a higher fitness of the heterozygotes. [ 5 ]


In  Gymnadenia rhellicani , flower pigmentation is controlled by changes to  amino acids  612 and 663 in GrMYB1, which plays a role in  anthocyanin  pigment production. Red flowers, heterozygous with black and white alleles, maintain a reproductive fitness advantage over white and black varieties presumably because they attract both bee and fly pollinator populations. Since the emergence of the white allele, the frequency of the red phenotype has been increasing in wild populations in multiple regions of the alps. [ 6 ]


Polar overdominance  is a type of overdominance where either only the paternal or maternal allele is being synthesized in the offspring. An example of this was illustrated by a famous  ram  named Solid Gold and his offspring. This ram was known for its callipyge phenotype (pronounced muscular features and hindquarters) caused by a mutated allele, but only 15% of its offspring received these same traits. Solid Gold’s offspring only expressed the same callipyge phenotype if they inherited the mutated allele from Solid Gold and a wildtype allele from their mother, which would result in a C pat /N mat  genotype. Offspring with genotypes such as: C pat /C mat , N pat /N mat , and N pat /C mat  did not express the callipyge phenotype. [ 7 ]


Population Geneticist  John H. Gillespie  established the following convention: [ 8 ]


Where h is the heterozygote effect and s is the recessive allele effect.
Thus given a value for s (i.e.: 0<s<1), h can yield the following information:


For the case of sickle cell anemia the situation corresponds to the case h<0 in the Gillespie Model.


[ 1 ] Paleopolyploidy  is the result of  genome duplications  which occurred at least several million years ago (MYA).  Such an event could either double the genome of a single species ( autopolyploidy ) or combine those of two species ( allopolyploidy ). Because of functional  redundancy , genes are rapidly silenced or lost from the duplicated genomes.  Most paleopolyploids, through evolutionary time, have lost their  polyploid  status through a process called  diploidization , and are currently considered  diploids , e.g.,  baker's yeast , [ 2 ]   Arabidopsis thaliana , [ 3 ]  and perhaps  humans . [ 4 ] [ 5 ] [ 6 ] [ 7 ]


Paleopolyploidy is extensively studied in plant lineages.  It has been found that almost all flowering plants have undergone at least one round of genome duplication at some point during their evolutionary history.  Ancient genome duplications are also found in the early ancestor of vertebrates (which includes the human lineage) near the origin of the  bony fishes , and another in the stem lineage of teleost fishes. [ 8 ]  Evidence suggests that baker's yeast ( Saccharomyces cerevisiae ), which has a compact genome, experienced polyploidization during its evolutionary history.


The term  mesopolyploid  is sometimes used for species that have undergone whole genome multiplication events (whole genome duplication, whole genome triplification, etc.) in more recent history, such as within the last 17 million years. [ 9 ]


Ancient genome duplications are widespread throughout  eukaryotic  lineages, particularly in plants. Studies suggest that the common ancestor of  Poaceae , the grass family which includes important crop species such as maize, rice, wheat, and sugar cane, shared a whole genome duplication about  70  million years ago . [ 10 ]  In more ancient monocot lineages one or likely multiple rounds of additional whole genome duplications had occurred, which were however not shared with the ancestral  eudicots . [ 11 ]  Further independent more recent whole genome duplications have occurred in the lineages leading to maize, sugar cane and wheat, but not rice, sorghum or foxtail millet. [ citation needed ]


A polyploidy event  160  million years ago  is theorized to have created the ancestral line that led to all modern flowering plants. [ 12 ]  That paleopolyploidy event was studied by sequencing the genome of an ancient flowering plant,  Amborella trichopoda . [ 13 ]


The core eudicots also shared a common whole genome triplication (paleo-hexaploidy), which was estimated to have occurred after  monocot - eudicot  divergence but before the divergence of  rosids  and  asterids . [ 14 ] [ 15 ] [ 16 ]  Many eudicot species have experienced additional whole genome duplications or triplications. For example, the model plant  Arabidopsis thaliana , the first plant to have its entire genome sequenced, has experienced at least two additional rounds of whole genome duplication since the duplication shared by the core eudicots. [ 3 ]  The most recent event took place before the divergence of the  Arabidopsis  and  Brassica  lineages, about  20  million years ago  to  45  million years ago . Other examples include the sequenced eudicot genomes of apple, soybean, tomato, cotton, etc. [ citation needed ]


Compared with plants, paleopolyploidy is much rarer in the animal kingdom.  It has been identified mainly in amphibians and bony fishes.  Although some studies suggested one or more common genome duplications are shared by all vertebrates (including humans), the evidence is not as strong as in the other cases because the duplications, if they exist, happened so long ago (about 400-500 Ma compared to less than 200 Ma in plants), and the matter is still under debate. The idea that vertebrates share a common whole genome duplication is known as the  2R Hypothesis . Many researchers are interested in the reason why animal lineages, particularly mammals, have had so many fewer whole genome duplications than plant lineages. [ citation needed ]


A well-supported paleopolyploidy has been found in baker's yeast ( Saccharomyces cerevisiae ), despite its small, compact genome (~13Mbp), after the divergence from  Kluyveromyces lactis  and  K. marxianus . [ 17 ]   Through genome streamlining, yeast has lost 90% of the duplicated genome over evolutionary time and is now recognized as a diploid organism. [ citation needed ]


Duplicated genes can be identified through  sequence homology  on the DNA or protein level.  Paleopolyploidy can be identified as massive gene duplication at one time using a  molecular clock .  To distinguish between whole-genome duplication and a collection of (more common) single  gene duplication  events, the following rules are often applied:


In theory, the two duplicated genes should have the same "age"; that is, the divergence of the sequence should be equal between the two genes duplicated by paleopolyploidy ( homeologs ).   Synonymous substitution  rate,  Ks , is often used as a molecular clock to determine the time of gene duplication. Thus, paleopolyploidy is identified as a "peak" on the duplicate number vs. Ks graph (shown on the right).


However, using Ks plots to identify and document ancient polyploid events can be problematic, as the method fails to identify genome duplications that were followed by massive gene elimination and genome refinement. Other mixed model approaches that combined Ks plots with other methods are being developed to better understand paleopolyploidy. [ 18 ]


Duplication events that occurred a long time ago in the history of various evolutionary lineages can be difficult to detect because of subsequent diploidization (such that a polyploid starts to behave cytogenetically as a diploid over time) as mutations and gene translations gradually make one copy of each chromosome unlike its counterpart.  This usually results in a low confidence for identifying a very ancient paleopolyploidy.


Paleopolyploidization events lead to massive cellular changes, including doubling of the genetic material, changes in gene expression and increased cell size.  Gene loss during diploidization is not completely random, but heavily selected.  Genes from large gene families are duplicated.  On the other hand, individual genes are not duplicated. [ clarification needed ]   Overall, paleopolyploidy can have both short-term and long-term evolutionary effects on an organism's fitness in the natural environment. [ citation needed ]


Whole genome duplication may increase the rates and efficiency by which organisms acquire new biological traits. However, one test of this hypothesis, which compared evolutionary rates in innovation in early teleost fishes (with duplicate genomes) to early holostean fishes (without duplicated genomes) found little difference between the two. [ 8 ]


Genome doubling provided the organism with redundant alleles that can evolve freely with little selection pressure.  The duplicated genes can undergo  neofunctionalization  or  subfunctionalization  which could help the organism adapt to the new environment or survive different stress conditions. [ citation needed ]


Polyploids often have larger cells and even larger organs.  Many important crops, including wheat, maize and  cotton , are paleopolyploids which were selected for domestication by ancient peoples. [ citation needed ]


It has been suggested that many polyploidization events created new species, via a gain of adaptive traits, or by sexual incompatibility with their diploid counterparts. An example would be the recent  speciation  of allopolyploid  Spartina  —  S. anglica ;  the polyploid plant is so successful that it is listed as an  invasive species  in many regions. [ 19 ]


There are two major divisions of  polyploidy , allopolyploidy and autopolyploidy.  Allopolyploids arise as a result of the hybridization of two related species, while autopolyploids arise from the duplication of a species' genome as a result of hybridization of two conspecific parents, [ 20 ]  or somatic doubling in reproductive tissue of a parent.  Allopolyploid species are believed to be much more prevalent in nature, [ 20 ]  possibly because allopolyploids inherit different genomes, resulting in increased  heterozygosity , and therefore higher fitness.  These different genomes result in an increased likelihood of large genomic reorganizations, [ 20 ] [ 21 ]  which can be either deleterious, or advantageous.  Autopolyploidy, however, is generally considered to be a neutral process, [ 21 ]  though it has been hypothesized that autopolyploidy may serve as a useful mechanism for inducing speciation, and therefore assisting in the ability of an organism to quickly colonize in new habitats without undergoing the time-intensive and costly period of genomic reorganization experienced by allopolyploid species.  One common source of autopolyploidy in plants stems from "perfect flowers", which are capable of self-pollination, or "selfing".  This, along with errors in  meiosis  that lead to  aneuploidy , can create an environment where autopolyploidy is very likely.  This fact can be exploited in a laboratory setting by using  colchicine  to inhibit  chromosome  segregation during meiosis, creating synthetic autopolyploid plants. [ citation needed ]


Following polyploidy events, there are several possible fates for duplicated  genes ; both copies may be retained as functional genes, change in gene function may occur in one or both copies,  gene silencing  may mask one or both copies, or complete gene loss may occur. [ 20 ] [ 22 ]  Polyploidy events will result in higher levels of heterozygosity, and, over time, can lead to an increase in the total number of functional genes in the genome.  As time passes after a genome duplication event, many genes will change function as a result of either change in duplicate gene function for both allo- and autopolyploid species, or there will be changes in gene expression caused by genomic rearrangements induced by genome duplication in allopolyploids.  When both copies of a gene are retained, and thus the number of copies doubled, there is a chance that there will be a proportional increase in expression of that gene, resulting in twice as much  mRNA  transcript being produced.  There is also the possibility that transcription of a duplicated gene will be down-regulated, resulting in less than two-fold increase in transcription of that gene, or that the duplication event will yield more than a two-fold increase in transcription. [ 23 ]   In one species,  Glycine dolichocarpa  (a close relative of the  soybean ,  Glycine max ), it has been observed that following a genome duplication roughly 500,000 years ago, there has been a 1.4 fold increase in transcription, indicating that there has been a proportional decrease in transcription relative to gene copy number following the duplication event. [ 23 ]


The hypothesis of vertebrate paleopolyploidy originated as early as the 1970s, proposed by the biologist  Susumu Ohno .  He reasoned that the vertebrate genome could not achieve its complexity without large scale whole-genome duplications.  The "two rounds of genome duplication" hypothesis ( 2R hypothesis ) came about, and gained in popularity, especially among developmental biologists. [ citation needed ]


Some researchers have questioned the 2R hypothesis because it predicts that vertebrate genomes should have a 4:1 gene ratio compared with invertebrate genomes, and this is not supported by findings from the 48 vertebrate genome projects available in mid-2011. For example, the human genome consists of ~21,000 protein coding genes according to June, 2011 counts at UCSC and Ensembl genome analysis centers [ citation needed ]  while an average invertebrate genome size is about 15,000 genes. The  amphioxus  genome sequence provided support for the hypothesis of two rounds of whole genome duplication, followed by loss of duplicate copies of most genes. [ 24 ]  Additional arguments against 2R were based on the lack of the (AB)(CD) tree topology amongst four members of a gene family in vertebrates. However, if the two genome duplications occurred close together, we would not expect to find this topology. [ 25 ]  A recent study generated the  sea lamprey  genetic map, which yielded strong support for the hypothesis that a single whole-genome duplication occurred in the basal vertebrate lineage, preceded and followed by several evolutionarily independent segmental duplications that occurred over chordate evolution. [ 26 ]


Particulate inheritance  is a pattern of inheritance discovered by  Mendelian genetics  theorists, such as  William Bateson ,  Ronald Fisher  or  Gregor Mendel  himself, showing that  phenotypic traits  can be passed from generation to generation through "discrete particles" known as  genes , which can keep their ability to be expressed while not always appearing in a descending generation. [ 1 ]


Early in the 19th century, scientists had already recognized that Earth has been inhabited by living creatures for a very long time. On the other hand, they did not understand what mechanisms actually drove  biological diversity . They also did not understand how  physical traits  are inherited from one generation to the next.  Blending inheritance  was the common ideal at the time, but was later discredited by the experiments of Gregor Mendel. Mendel proposed the theory of particulate inheritance by using  pea  plants ( Pisum sativum ) to explain how variation can be inherited and maintained over time. [ citation needed ]


Since Mendel used experimental methods to devise his particulate inheritance theory, he developed three basic laws of inheritance: the  Law of Segregation , the  Law of Independent Assortment , and the  Law of Dominance : [ 2 ]


Mendel's experiment with tall and short pea plants demonstrates how each individual plant has two particles called  alleles . When a pea plant produces  gametes  (reproductive cells), it segregates one allele to each one. [ citation needed ]


The law states that when the parents differ from each other in two or more pairs of contrasting characters, the inheritance of one pair of characters is independent to that of the other pair of characters. [ citation needed ]


In the pea plants, Mendel observed that the "T" allele ( dominant ) masked the effects of the "t" allele ( recessive ). The terms "dominant" and "recessive" are used for the masking and the covered allele, respectively. All offspring from this cross are  heterozygotes  in terms of their  genotypes . They also are tall (because the allele for tall masks the allele for short) in terms of their " phenotype ". [ 3 ]


In a 1918 publication titled "The Supposition of Mendelian Inheritance Among Close Relatives,"  R.A. Fisher  showed that particulate inheritance was capable of generating the vast amount of variation we see among closely related individuals. This helped to reconcile the Biometric and Mendelian schools of thought at the time, and was an important step in the  modern synthesis . [ 4 ]


A  pedigree chart  is a diagram that shows the occurrence of certain traits through different generations of a family, [ 1 ] [ 2 ]  most commonly for  humans , show  dogs , and race  horses . [ citation needed ]


The word pedigree is a corruption of the Anglo-Norman French  pé de grue  or "crane's foot", either because the typical lines and split lines (each split leading to different offspring of the one parent line) resemble the thin leg and foot of a  crane [ 3 ]  or because such a mark was used to denote succession in pedigree charts. [ 4 ]


A pedigree results in the presentation of family information in the form of an easily readable chart. It can be simply called a " family tree ". Pedigrees use a standardized set of symbols, squares represent males and circles represent females. Pedigree construction is a family history, and details about an earlier generation may be uncertain as memories fade. If the sex of the person is unknown, a diamond is used. Someone with the  phenotype  (trait) in question is represented by a filled-in (darker) symbol.  Heterozygotes , when identifiable, are indicated by a shaded dot inside a symbol or a half-filled symbol.


Relationships in a pedigree are shown as a series of lines. A horizontal line connects parents and a vertical line leads to their offspring. The offspring are connected by a horizontal sibship line and listed in birth order from left to right. If the offspring are twins then they will be connected by a triangle. If an offspring dies then its symbol will be crossed by a line. If the offspring is stillborn or aborted, it is represented by a small triangle.


Each generation is identified by a  Roman numeral  (I, II, III, and so on), and each individual within the same generation is identified by an  Arabic numeral  (1, 2, 3, and so on). Analysis of the pedigree using the principles of  Mendelian inheritance  can determine whether a trait has a dominant or recessive pattern of inheritance. Pedigrees are often constructed after a family member afflicted with a genetic disorder has been identified. This individual, known as the  proband , is indicated on the pedigree by an arrow. [ 5 ]  These changes may occur yearly or monthly.


In  England  and  Wales  pedigrees are officially recorded in the  College of Arms , which has records going back to the Middle Ages, including pedigrees collected during roving inquiries by its  heralds  during the sixteenth and seventeenth centuries. The purpose of these  heraldic visitations  was to register and regulate the use of  coats of arms . Those who claimed the right to bear arms had to provide proof either of a grant of arms to them by the College, or of descent from an ancestor entitled to arms. It was for this reason that pedigrees were recorded by the visitations. Pedigrees continue to be registered at the College of Arms and kept up to date on a voluntary basis but are not accessible to the general public without payment of a fee.


More visible, therefore, are the pedigrees recorded in published works, such as  Burke's Peerage  and Burke's  Landed Gentry  in the United Kingdom and, in continental  Europe  by the  Almanach de Gotha .


A pedigree may be used to establish the probability of a child having a particular disorder or condition. It may be used to discover where the genes in question are located (x, y, or autosome chromosome), and to determine whether a trait is dominant or recessive. When a pedigree shows a condition appearing in a 50:50 ratio between men and women, it is considered  autosomal . When the condition predominantly affects males in the pedigree, it is considered  x-linked . [ 6 ]


Some examples of dominant traits include  male baldness ,  astigmatism , and  dwarfism . Some examples of recessive traits include small eyes, little body hair, and tall stature. [ 7 ]


In the practice of  selective breeding  of animals, particularly in  animal fancy  and  livestock , including  horses , pedigree charts are used to track the ancestry of animals and assist in the planning of suitable  breeding programs  to enhance desirable traits.  Breed registries  are formed and are dedicated to the accurate tracking of pedigrees and maintaining accurate records of birth, death, and identifying characteristics of each registered animal. [ 8 ]


A  phenotypic trait , [ 1 ] [ 2 ]  simply  trait , or  character state [ 3 ] [ 4 ]  is a distinct variant of a  phenotypic  characteristic of an  organism ; it may be either  inherited  or determined environmentally, but typically occurs as a combination of the two. [ 5 ]   For example, having  eye color  is a  character  of an organism,   while blue, brown and hazel versions of eye color are  traits .  The term  trait  is generally used in  genetics , often to describe phenotypic expression of different combinations of  alleles  in different individual organisms within a single  population , such as the famous purple vs. white flower coloration in  Gregor Mendel 's pea plants.  By contrast, in  systematics , the term   character state  is employed to describe features that represent fixed diagnostic differences among  taxa , such as the absence of tails in  great apes , relative to other  primate  groups. [ 6 ]


A  phenotypic  trait is an obvious, observable, and measurable characteristic of an organism; it is the expression of genes in an observable way. An example of a phenotypic trait is a specific hair color or eye color. Underlying genes, that make up the  genotype , determine the hair color, but the hair color observed is the phenotype.


The phenotype is dependent on the genetic make-up of the organism, but is also influenced by the environmental conditions  that the organism was subjected to during its  ontogenetic  development, [ 7 ]  including various  epigenetic  processes.


Regardless of the degree of influence of genotype versus environment, the phenotype encompasses all of the characteristics of an organism, including traits at multiple  levels of biological organization , ranging from  behavior  and  evolutionary history of life  traits (e.g., litter size), through morphology (e.g., body height and composition), physiology (e.g., blood pressure), cellular characteristics (e.g., membrane lipid composition, mitochondrial densities), components of  biochemical  pathways, and even  messenger RNA . [ citation needed ]


Different phenotypic traits are caused by different forms of  genes , or  alleles , which arise by  mutation  in a single individual and are passed on to successive generations. [ 8 ]


The  biochemistry  of the intermediate proteins determines how they interact in the cell. Therefore, biochemistry  predicts  how different combinations of alleles will produce varying traits. [ citation needed ]


Extended expression patterns seen in diploid organisms include facets of  incomplete dominance ,  codominance , and  multiple alleles . Incomplete dominance is the condition in which neither allele dominates the other in one heterozygote. Instead the phenotype is intermediate in heterozygotes. Thus you can tell that each allele is present in the heterozygote. [ 9 ]  Codominance refers to the allelic relationship that occurs when two alleles are both expressed in the heterozygote, and both phenotypes are seen simultaneously. [ 10 ]  Multiple alleles refers to the situation when there are more than 2 common alleles of a particular gene. Blood groups in humans is a classic example. The  ABO blood group  proteins are important in
determining blood type in humans, and this is determined by different alleles of the one locus. [ 11 ]


Schizotypy  is an example of a psychological phenotypic trait found in schizophrenia-spectrum disorders. Studies have shown that gender and age influences the expression of schizotypal traits. [ 12 ]  For instance, certain schizotypal traits may develop further during adolescence, whereas others stay the same during this period. [ 12 ]


Ploidy  ( / ˈ p l ɔɪ d i / ) is the number of complete sets of  chromosomes  in a  cell , and hence the number of possible  alleles  for  autosomal  and  pseudoautosomal   genes . Here  sets of chromosomes  refers to the number of maternal and paternal chromosome copies, respectively, in each homologous chromosome pair—the form in which chromosomes naturally exist.  Somatic cells ,  tissues , and  individual  organisms can be described according to the number of sets of chromosomes present (the "ploidy level"):  monoploid  (1 set),  diploid  (2 sets),  triploid  (3 sets),  tetraploid  (4 sets),  pentaploid  (5 sets),  hexaploid  (6 sets),  heptaploid [ 2 ]  or  septaploid [ 3 ]  (7 sets), etc. The generic term  polyploid  is often used to describe cells with three or more sets of chromosomes. [ 4 ] [ 5 ]


Virtually all  sexually reproducing  organisms are made up of somatic cells that are diploid or greater, but ploidy level may vary widely between different organisms, between different tissues within the same organism, and at different stages in an organism's life cycle. Half of all known plant genera contain polyploid species, and about two-thirds of all grasses are polyploid. [ 6 ]  Many animals are uniformly diploid, though polyploidy is common in invertebrates, reptiles, and amphibians. In some species, ploidy varies between individuals of the same species (as in the  social insects ), and in others entire tissues and organ systems may be polyploid despite the rest of the body being diploid (as in the mammalian  liver [ citation needed ] ). For many organisms, especially plants and fungi, changes in ploidy level between generations are major drivers of  speciation . In mammals and birds, ploidy changes are typically fatal. [ 7 ]  There is, however, evidence of polyploidy in organisms now considered to be diploid, suggesting that polyploidy has contributed to evolutionary diversification in plants and animals through successive rounds of polyploidization and rediploidization. [ 8 ] [ 9 ]


Humans are diploid organisms, normally carrying two complete sets of chromosomes in their somatic cells: one copy of paternal and maternal chromosomes, respectively, in each of the 23 homologous pairs of chromosomes that humans normally have. This results in two homologous pairs within each of the 23 homologous pairs,  providing a full complement of 46 chromosomes. This total number of individual chromosomes (counting all complete sets) is called the  chromosome number  or  chromosome complement . The number of chromosomes found in a single complete set of chromosomes is called the  monoploid number  ( x ). The  haploid number  ( n ) refers to the total number of chromosomes found in a  gamete  (a  sperm  or  egg  cell produced by  meiosis  in preparation for sexual reproduction). Under normal conditions, the haploid number is exactly half the total number of chromosomes present in the organism's somatic cells, with one paternal and maternal copy in each chromosome pair. For diploid organisms, the monoploid number and haploid number are equal; in humans, both are equal to 23. When a human  germ cell  undergoes meiosis, the diploid 46 chromosome complement is split in half to form haploid gametes. After fusion of a male and a female gamete (each containing 1 set of 23 chromosomes) during  fertilization , the resulting  zygote  again has the full complement of 46 chromosomes: 2 sets of 23 chromosomes.  Euploidy and aneuploidy  describe having a number of chromosomes that is an exact multiple of the number of chromosomes in a normal gamete; and having any other number, respectively. For example, a person with  Turner syndrome  may be missing one sex chromosome (X or Y), resulting in a (45,X) karyotype instead of the usual (46,XX) or (46,XY). This is a type of aneuploidy and cells from the person may be said to be aneuploid with a (diploid) chromosome complement of 45.


The term  ploidy  is a  back-formation  from  haploidy  and  diploidy . "Ploid" is a combination of Ancient Greek -πλόος (-plóos, "-fold") and -ειδής (- eidḗs ), from εἶδος ( eîdos , "form, likeness"). [ a ]  The principal meaning of the  Greek  word ᾰ̔πλόος (haplóos) is "single", [ 10 ]  from ἁ- (ha-, "one, same"). [ 11 ]  διπλόος ( diplóos ) means "duplex" or "two-fold". Diploid therefore means "duplex-shaped" (compare "humanoid", "human-shaped").


Polish-German botanist  Eduard Strasburger  coined the terms  haploid  and  diploid  in 1905. [ b ]  Some authors suggest that Strasburger based the terms on  August Weismann 's conception of the id (or  germ plasm ), [ 14 ] [ 15 ] [ 16 ]  hence haplo- id  and diplo- id . The two terms were brought into the English language from German through  William Henry Lang 's 1908 translation of a 1906 textbook by Strasburger and colleagues. [ 17 ] [ citation needed ]


The term  haploid  is used with two distinct but related definitions. In the most generic sense, haploid refers to having the number of sets of chromosomes normally found in a  gamete . [ 18 ]  Because two gametes necessarily combine during sexual reproduction to form a single zygote from which somatic cells are generated, healthy gametes always possess exactly half the number of sets of chromosomes found in the somatic cells, and therefore "haploid" in this sense refers to having exactly half the number of sets of chromosomes found in a somatic cell. By this definition, an organism whose gametic cells contain a single copy of each chromosome (one set of chromosomes) may be considered haploid while the somatic cells, containing two copies of each chromosome (two sets of chromosomes), are diploid. This scheme of diploid somatic cells and haploid gametes is widely used in the animal kingdom and is the simplest to illustrate in diagrams of genetics concepts. But this definition also allows for haploid gametes with  more than one  set of chromosomes. As given above, gametes are by definition haploid, regardless of the actual number of sets of chromosomes they contain. An organism whose somatic cells are tetraploid (four sets of chromosomes), for example, will produce gametes by meiosis that contain two sets of chromosomes. These gametes might still be called haploid even though they are numerically diploid. [ citation needed ]


An alternative usage defines "haploid" as having a single copy of each chromosome – that is, one and only one set of chromosomes. [ 19 ]  In this case, the nucleus of a  eukaryotic  cell is said to be haploid only if it has a single set of  chromosomes , each one not being part of a pair. By extension a cell may be called haploid if its nucleus has one set of chromosomes, and an organism may be called haploid if its body cells (somatic cells) have one set of chromosomes per cell. By this definition haploid therefore would not be used to refer to the gametes produced by the tetraploid organism in the example above, since these gametes are numerically diploid. The term  monoploid  is often used as a less ambiguous way to describe a single set of chromosomes; by this second definition, haploid and monoploid are identical and can be used interchangeably. [ citation needed ]


Gametes  ( sperm  and  ova ) are haploid cells. The haploid gametes produced by most organisms combine to form a  zygote  with  n  pairs of chromosomes, i.e. 2 n  chromosomes in total. The chromosomes in each pair, one of which comes from the sperm and one from the egg, are said to be  homologous . Cells and organisms with pairs of homologous chromosomes are called diploid. For example, most animals are diploid and produce haploid gametes. During  meiosis , sex cell precursors have their number of chromosomes halved by randomly "choosing" one member of each pair of chromosomes, resulting in haploid gametes. Because homologous chromosomes usually differ genetically, gametes usually differ genetically from one another. [ 20 ]


All  plants  and many  fungi  and  algae  switch between a haploid and a diploid state, with one of the stages emphasized over the other. This is called  alternation of generations . Most fungi and algae are haploid during the principal stage of their life cycle, as are some primitive plants like  mosses . More recently evolved plants, like the  gymnosperms  and  angiosperms , spend the majority of their life cycle in the diploid stage. Most animals are diploid, but male  bees ,  wasps , and  ants  are haploid organisms because they develop from unfertilized, haploid eggs, while females (workers and queens) are diploid, making their system  haplodiploid . [ citation needed ]


In some cases there is evidence that the  n  chromosomes in a haploid set have resulted from duplications of an originally smaller set of chromosomes. This "base" number – the number of apparently originally unique chromosomes in a haploid set – is called the  monoploid number , [ 21 ]  also known as  basic  or  cardinal number , [ 22 ]  or  fundamental number . [ 23 ] [ 24 ]  As an example, the chromosomes of  common wheat  are believed to be derived from three different ancestral species, each of which had 7 chromosomes in its haploid gametes. The monoploid number is thus 7 and the haploid number is 3 × 7 = 21. In general  n  is a multiple of  x . The somatic cells in a wheat plant have six sets of 7 chromosomes: three sets from the egg and three sets from the sperm which fused to form the plant, giving a total of 42 chromosomes. As a formula, for wheat 2 n  = 6 x  = 42, so that the haploid number  n  is 21 and the monoploid number  x  is 7. The gametes of common wheat are considered to be haploid, since they contain half the genetic information of somatic cells, but they are not monoploid, as they still contain three complete sets of chromosomes ( n  = 3 x ). [ 25 ]


In the case of wheat, the origin of its haploid number of 21 chromosomes from three sets of 7 chromosomes can be demonstrated. In many other organisms, although the number of chromosomes may have originated in this way, this is no longer clear, and the monoploid number is regarded as the same as the haploid number. Thus in humans,  x  =  n  = 23.


Diploid  cells have two  homologous  copies of each  chromosome , usually one from the  mother  and one from the  father . All or nearly all mammals are diploid organisms. The suspected tetraploid (possessing four-chromosome sets) plains viscacha rat ( Tympanoctomys barrerae ) and golden viscacha rat ( Pipanacoctomys aureus ) [ 26 ]  have been regarded as the only known exceptions (as of 2004). [ 27 ]  However, some genetic studies have rejected any  polyploidism  in mammals as unlikely, and suggest that amplification and dispersion of repetitive sequences best explain the large genome size of these two rodents. [ 28 ]  All normal diploid individuals have some small fraction of cells that display  polyploidy .  Human  diploid cells have 46 chromosomes (the  somatic  number,  2n ) and human haploid  gametes  (egg and sperm) have 23 chromosomes ( n ).  Retroviruses  that contain two copies of their RNA genome in each viral particle are also said to be diploid. Examples include  human foamy virus ,  human T-lymphotropic virus , and  HIV . [ 29 ]


Polyploidy  is the state where all cells have multiple sets of chromosomes beyond the basic set, usually 3 or more. Specific terms are  triploid  (3 sets),  tetraploid  (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid [ 2 ]  or septaploid [ 3 ]  (7 sets), octoploid (8 sets), nonaploid (9 sets), decaploid (10 sets), undecaploid (11 sets), dodecaploid (12 sets), tridecaploid (13 sets), tetradecaploid (14 sets), etc. [ 30 ] [ 31 ] [ 32 ] [ 33 ]  Some higher ploidies include hexadecaploid (16 sets), dotriacontaploid (32 sets), and tetrahexacontaploid (64 sets), [ 34 ]  though Greek terminology may be set aside for readability in cases of higher ploidy (such as "16-ploid"). [ 32 ]   Polytene chromosomes  of plants and fruit flies can be 1024-ploid. [ 35 ] [ 36 ]  Ploidy of systems such as the  salivary gland ,  elaiosome ,  endosperm , and  trophoblast  can exceed this, up to 1048576-ploid in the silk glands of the commercial silkworm  Bombyx mori . [ 37 ]


The chromosome sets may be from the same species or from closely related species. In the latter case, these are known as allopolyploids (or amphidiploids, which are allopolyploids that behave as if they were normal diploids). Allopolyploids are formed from the hybridization of two separate species. In plants, this probably most often occurs from the pairing of meiotically unreduced  gametes , and not by diploid–diploid hybridization followed by chromosome doubling. [ 38 ]  The so-called  Brassica  triangle  is an example of allopolyploidy, where three different parent species have hybridized in all possible pair combinations to produce three new species. [ 39 ]


Polyploidy occurs commonly in plants, but rarely in animals. Even in diploid organisms, many  somatic cells  are polyploid due to a process called  endoreduplication , where duplication of the  genome  occurs without  mitosis  (cell division). The extreme in polyploidy occurs in the  fern  genus  Ophioglossum , the adder's-tongues, in which polyploidy results in chromosome counts in the hundreds, or, in at least one case, well over one thousand. [ citation needed ]


It is possible for polyploid organisms to revert to lower ploidy by  haploidisation . [ citation needed ]


Polyploidy  is a characteristic of the bacterium  Deinococcus radiodurans   [ 40 ]  and of the  archaeon   Halobacterium salinarum . [ 41 ]  These two species are highly resistant to  ionizing radiation  and  desiccation , conditions that induce  DNA  double-strand breaks. [ 42 ] [ 43 ]  This resistance appears to be due to efficient  homologous recombinational  repair.


Depending on growth conditions,  prokaryotes  such as  bacteria  may have a chromosome copy number of 1 to 4, and that number is commonly fractional, counting portions of the chromosome partly replicated at a given time. This is because under exponential growth conditions the cells are able to replicate their DNA faster than they can divide. [ citation needed ]


In ciliates, the macronucleus is called  ampliploid , because only part of the genome is amplified. [ 44 ]


Mixoploidy is the case where two cell lines, one diploid and one polyploid,  coexist within the same organism . Though polyploidy in humans is not viable, mixoploidy has been found in live adults and children. [ 45 ]  There are two types: diploid-triploid mixoploidy, in which some cells have 46 chromosomes and some have 69, [ 46 ]  and diploid-tetraploid mixoploidy, in which some cells have 46 and some have 92 chromosomes. It is a major topic of cytology.


Dihaploid and polyhaploid cells are formed by  haploidisation  of polyploids, i.e., by halving the chromosome constitution. [ citation needed ]


Dihaploids (which are diploid) are important for selective breeding of tetraploid crop plants (notably potatoes), because selection is faster with diploids than with tetraploids. Tetraploids can be reconstituted from the diploids, for example by somatic fusion. [ citation needed ]


The term "dihaploid" was coined by Bender [ 47 ]  to combine in one word the number of genome copies (diploid) and their origin (haploid). The term is well established in this original sense, [ 48 ] [ 49 ]  but it has also been used for doubled monoploids or  doubled haploids , which are homozygous and used for genetic research. [ 50 ]


Euploidy  ( Greek   eu , "true" or "even") is the state of a cell or organism having one or more than one set of the same set of chromosomes, possibly excluding the  sex-determining chromosomes . For example, most human cells have 2 of each of the 23 homologous monoploid chromosomes, for a total of 46 chromosomes. A human cell with one extra set of the 23 normal chromosomes (functionally triploid) would be considered euploid. Euploid  karyotypes  would consequentially be a multiple of the  haploid number , which in humans is 23. [ citation needed ]


Aneuploidy  is the state where one or more individual chromosomes of a normal set are absent or present in more than their usual number of copies (excluding the absence or presence of complete sets, which is considered euploidy). Unlike euploidy, aneuploid karyotypes will not be a multiple of the haploid number. In humans, examples of aneuploidy include having a single extra chromosome (as in  Down syndrome , where affected individuals have three copies of chromosome 21) or missing a chromosome (as in  Turner syndrome , where affected individuals have only one sex chromosome). Aneuploid  karyotypes  are given names with the suffix  -somy  (rather than  -ploidy , used for euploid karyotypes), such as  trisomy  and  monosomy . [ citation needed ]


Homoploid means "at the same ploidy level", i.e. having the same number of  homologous chromosomes . For example, homoploid  hybridization  is hybridization where the offspring have the same ploidy level as the two parental species. This contrasts with a common situation in plants where chromosome doubling accompanies or occurs soon after hybridization. Similarly, homoploid speciation contrasts with  polyploid speciation . [ citation needed ]


Zygoidy is the state in which the chromosomes are paired and can undergo meiosis. The zygoid state of a species may be diploid or polyploid. [ 51 ] [ 52 ]  In the azygoid state the chromosomes are unpaired. It may be the natural state of some asexual species or may occur after meiosis. In diploid organisms the azygoid state is monoploid. (See below for dihaploidy.)


In the strictest sense, ploidy refers to the number of sets of chromosomes in a single  nucleus  rather than in the cell as a whole. Because in most situations there is only one nucleus per cell, it is commonplace to speak of the ploidy of a cell, but in cases in which there is more than one nucleus per cell, more specific definitions are required when ploidy is discussed. Authors may at times report the total combined ploidy of all nuclei present within the cell membrane of a  syncytium , [ 37 ]  though usually the ploidy of each nucleus is described individually. For example, a fungal  dikaryon  with two separate haploid nuclei is distinguished from a diploid cell in which the chromosomes share a nucleus and can be shuffled together. [ 53 ]


It is possible on rare occasions for ploidy to increase in the  germline , which can result in  polyploid  offspring and ultimately polyploid species. This is an important evolutionary mechanism in both plants and animals and is known as a primary driver of  speciation . [ 8 ]  As a result, it may become desirable to distinguish between the ploidy of a species or variety as it presently breeds and that of an ancestor. The number of chromosomes in the ancestral (non-homologous) set is called the  monoploid number  ( x ), and is distinct from the haploid number ( n ) in the organism as it now reproduces. [ citation needed ]


Common wheat  ( Triticum aestivum ) is an organism in which  x  and  n  differ. Each plant has a total of six sets of chromosomes (with two sets likely having been obtained from each of three different diploid species that are its distant ancestors). The somatic cells are hexaploid, 2 n  = 6 x  = 42 (where the monoploid number  x  = 7 and the haploid number  n  = 21). The gametes are haploid for their own species, but triploid, with three sets of chromosomes, by comparison to a probable evolutionary ancestor,  einkorn wheat . [ citation needed ]


Tetraploidy  (four sets of chromosomes, 2 n  = 4 x ) is common in many  plant  species, and also occurs in  amphibians ,  reptiles , and  insects . For example, species of  Xenopus  (African toads) form a  ploidy series , featuring diploid ( X. tropicalis , 2n=20), tetraploid ( X. laevis , 4n=36), octaploid ( X. wittei , 8n=72), and dodecaploid ( X. ruwenzoriensis , 12n=108) species. [ 54 ]


Over evolutionary time scales in which  chromosomal polymorphisms  accumulate, these changes become less apparent by  karyotype  – for example, humans are generally regarded as diploid, but the  2R hypothesis  has confirmed two rounds of whole genome duplication in early vertebrate ancestors. [ citation needed ]


Ploidy can also vary between individuals of the same species or at different stages of the  life cycle . [ 55 ] [ 56 ]  In some insects it differs by  caste . In humans, only the gametes are haploid, but in many of the  social insects , including  ants ,  bees , and  termites , males develop from unfertilized eggs, making them haploid for their entire lives, even as adults. [ citation needed ]


In the Australian bulldog ant,  Myrmecia pilosula , a haplodiploid species, haploid individuals of this species have a single chromosome and diploid individuals have two chromosomes. [ 57 ]  In  Entamoeba , the ploidy level varies from 4 n  to 40 n  in a single population. [ 58 ]   Alternation of generations  occurs in most plants, with individuals "alternating" ploidy level between different stages of their sexual life cycle. [ citation needed ]


In large multicellular organisms, variations in ploidy level between different tissues, organs, or cell lineages are common. Because the chromosome number is generally reduced only by the specialized process of meiosis, the somatic cells of the body inherit and maintain the chromosome number of the zygote by mitosis. However, in many situations somatic cells double their copy number by means of  endoreduplication  as an aspect of  cellular differentiation . For example, the hearts of two-year-old human children contain 85% diploid and 15% tetraploid nuclei, but by 12 years of age the proportions become approximately equal, and adults examined contained 27% diploid, 71% tetraploid and 2% octaploid nuclei. [ 59 ]


There is continued study and debate regarding the fitness advantages or disadvantages conferred by different ploidy levels. A study comparing the  karyotypes  of endangered or invasive plants with those of their relatives found that being polyploid as opposed to diploid is associated with a 14% lower risk of being endangered, and a 20% greater chance of being invasive. [ 60 ]  Polyploidy may be associated with increased vigor and adaptability. [ 61 ]  Some studies suggest that selection is more likely to favor diploidy in host species and haploidy in parasite species. [ 62 ]  However, polyploidization is associated with an increase in  transposable element  content [ 63 ] [ 64 ]  and relaxed  purifying selection  on  recessive  deleterious alleles. [ 65 ] [ 66 ]


When a germ cell with an uneven number of chromosomes undergoes meiosis, the chromosomes cannot be evenly divided between the daughter cells, resulting in  aneuploid  gametes. Triploid organisms, for instance, are usually sterile. Because of this, triploidy is commonly exploited in agriculture to produce seedless fruit such as bananas and watermelons. If the fertilization of human gametes results in three sets of chromosomes, the condition is called  triploid syndrome . [ citation needed ]


In  unicellular organisms  the  ploidy nutrient limitation hypothesis  suggests that  nutrient limitation  should encourage haploidy in preference to higher ploidies. This hypothesis is due to the higher  surface-to-volume ratio  of haploids, which eases nutrient uptake, thereby increasing the internal nutrient-to-demand ratio. Mable 2001 finds  Saccharomyces cerevisiae  to be somewhat inconsistent with this hypothesis however, as haploid growth is faster than diploid under high nutrient conditions. The NLH is also tested in haploid, diploid, and polyploid fungi by Gerstein et al. 2017. This result is also more complex: On the one hand, under  phosphorus  and other nutrient limitation, lower ploidy is selected as expected. However under normal nutrient levels or under limitation of only  nitrogen , higher ploidy was selected. Thus the NLH – and more generally, the idea that haploidy is selected by harsher conditions – is cast into doubt by these results. [ 67 ]


Older WGDs have also been investigated. Only as recently as 2015 was the ancient  whole genome duplication  in  Baker's yeast  proven to be  allopolyploid , by Marcet-Houben and Gabaldón 2015. It still remains to be explained why there are not more polyploid events in fungi, and the place of  neopolyploidy  and  mesopolyploidy  in  fungal history . [ 67 ]


The concept that those  genes  of an organism that are expressed exclusively in the diploid stage are under less efficient  natural selection  than those genes expressed in the  haploid  stage is referred to as the “masking theory”. [ 68 ]   Evidence in support of this masking theory has been reported in studies of the single-celled yeast  Saccharomyces cerevisiae . [ 69 ]   In further support of the masking theory, evidence of strong purifying selection in haploid tissue-specific genes has been reported for the plant  Scots Pine . [ 68 ]


The common  potato  ( Solanum tuberosum ) is an example of a tetraploid organism, carrying four sets of chromosomes. During sexual reproduction, each potato plant inherits two sets of 12 chromosomes from the pollen parent, and two sets of 12 chromosomes from the ovule parent. The four sets combined provide a full complement of 48 chromosomes. The haploid number (half of 48) is 24. The monoploid number equals the total chromosome number divided by the ploidy level of the somatic cells: 48 chromosomes in total divided by a ploidy level of 4 equals a monoploid number of 12. Hence, the monoploid number (12) and haploid number (24) are distinct in this example. [ citation needed ]


However, commercial potato crops (as well as many other crop plants) are commonly propagated  vegetatively  (by asexual reproduction through mitosis), [ 70 ]  in which case new individuals are produced from a single parent, without the involvement of gametes and fertilization, and all the offspring are genetically identical to each other and to the parent, including in chromosome number. The parents of these vegetative clones may still be capable of producing haploid gametes in preparation for sexual reproduction, but these gametes are not used to create the vegetative offspring by this route.


Some eukaryotic genome-scale or  genome size  databases and other sources which may list the ploidy levels of many organisms:


A  polygene  is a member of a group of non- epistatic   genes  that interact additively to influence a  phenotypic  trait, thus contributing to  multiple-gene inheritance  ( polygenic inheritance ,  multigenic inheritance, quantitative inheritance [ 1 ] ), a type of  non-Mendelian inheritance , as opposed to single-gene inheritance, which is the core notion of  Mendelian inheritance . The term "monozygous" is usually used to refer to a hypothetical gene as it is often difficult to distinguish the effect of an individual gene from the effects of other genes and the environment on a particular phenotype. Advances in statistical methodology and high throughput sequencing are, however, allowing researchers to locate candidate genes for the trait. In the case that such a gene is identified, it is referred to as a  quantitative trait locus  (QTL). These genes are generally  pleiotropic  as well. The genes that contribute to type 2  diabetes  are thought to be mostly polygenes. [ 2 ]  In July 2016, scientists reported identifying a set of 355  genes  from the  last universal common ancestor  (LUCA) of all  organisms  living on Earth. [ 3 ]


Traits with polygenic determinism correspond to the classical  quantitative characters , as opposed to the qualitative characters with monogenic or oligogenic determinism. In essence instead of two options, such as freckles or no freckles, there are many variations, like the color of skin, hair, or even eyes.


Polygenic locus   is any individual locus which is included in the system of genes responsible for the genetic component of variation in a quantitative (polygenic) character. Allelic substitutions contribute to the variance in a specified quantitative character. Polygenic locus may be either a single or complex genetic locus in the conventional sense, i.e., either a single gene or closely linked block of functionally related genes. [ 4 ]


In modern sense, the inheritance mode of polygenic patterns is called  polygenic inheritance , whose  main properties may be summarized as follows:


Polygenic inheritance  occurs when one characteristic is controlled by two or more  genes .  Often the genes are large in quantity but small in effect. [ 9 ]  Examples of human polygenic inheritance are height, skin color, eye color and weight. Polygenes exist in other organisms, as well.   Drosophila , for instance, display polygeny with traits such as wing morphology, [ 10 ]  bristle count [ 11 ]  and many others.


The frequency of the phenotypes of these traits generally follows a normal continuous variation distribution pattern. This results from the many possible allelic combinations. When the values are plotted, a  bell-shaped "normal" curve  is obtained. The  mode  of the distribution represents the optimal, or fittest, phenotype. The more genes are involved, the smoother the estimated curve, which follows from the  Central Limit Theorem . This implies that traits such as height that are both highly heritable and normally distributed are necessarily polygenic. In other words, the fact that human height follows a  smooth bell curve implies that there can be no single gene (or even small cluster of genes) that control height under ordinary circumstances. However, in this model all genes must code for alleles with additive effects. This assumption is often unrealistic as many genes display  epistasis  effects which can have unpredictable effects on the distribution of outcomes, especially when looking at the distribution on a fine scale. [ 12 ]


Traditionally, mapping polygenes requires statistical tools available to help measure the effects of polygenes as well as narrow in on single genes.  One of these tools is  QTL-mapping .  QTL-mapping utilizes a phenomenon known as  linkage disequilibrium  by comparing known marker genes with correlated phenotypes. Often, researchers will find a large region of DNA, called a  locus , that accounts for a significant amount of the variation observed in the measured trait. This locus will usually contain a large number of genes that are responsible. A new form of QTL has been described as  expression QTL  (eQTL). eQTLs regulate the amount of expressed mRNA, which in turn regulates the amount of protein within the organism. [ 13 ]


Another interest of statistical geneticists using QTL mapping is to determine the complexity of the genetic architecture underlying a phenotypic trait.  For example, they may be interested in knowing whether a phenotype is shaped by many independent loci, or by a few loci, and do those loci interact.  This can provide information on how the phenotype may be evolving.


Polyploidy  is a condition in which the  cells  of an  organism  have more than two paired sets of ( homologous )  chromosomes . Most species whose cells have  nuclei  ( eukaryotes ) are  diploid , meaning they have two complete sets of chromosomes, one from each of two parents; each set contains the same number of chromosomes, and the chromosomes are joined in pairs of homologous chromosomes. However, some organisms are  polyploid . Polyploidy is especially common in plants. Most eukaryotes have diploid  somatic cells , but produce  haploid   gametes  (eggs and sperm) by  meiosis . A  monoploid  has only one set of chromosomes, and the term is usually only applied to cells or organisms that are normally diploid. Males of  bees  and other  Hymenoptera , for example, are monoploid. Unlike animals,  plants  and multicellular  algae  have  life cycles  with two  alternating multicellular generations . The  gametophyte  generation is haploid, and produces gametes by  mitosis ; the  sporophyte  generation is diploid and produces  spores  by  meiosis .


Polyploidy is the result of whole-genome duplication during the evolution of species. It may occur due to abnormal  cell division , either during mitosis, or more commonly from the failure of chromosomes to separate during meiosis or from the fertilization of an egg by more than one sperm. [ 1 ]  In addition, it can be induced in plants and  cell cultures  by some chemicals: the best known is  colchicine , which can result in chromosome doubling, though its use may have other less obvious consequences as well.  Oryzalin  will also double the existing chromosome content.


Among  mammals , a high frequency of polyploid cells is found in organs such as the brain, liver, heart, and bone marrow. [ 2 ]  It also occurs in the somatic cells of other  animals , such as  goldfish , [ 3 ]   salmon , and  salamanders . It is common among  ferns  and flowering  plants  (see  Hibiscus rosa-sinensis ), including both wild and cultivated  species .  Wheat , for example, after millennia of  hybridization  and modification by humans, has strains that are  diploid  (two sets of chromosomes),  tetraploid  (four sets of chromosomes) with the common name of  durum  or macaroni wheat, and  hexaploid  (six sets of chromosomes) with the common name of bread wheat. Many agriculturally important plants of the genus  Brassica  are also tetraploids.  Sugarcane  can have ploidy levels higher than  octaploid . [ 4 ]


Polyploidization can be a mechanism of  sympatric speciation  because polyploids are usually unable to interbreed with their diploid ancestors. An example is the plant  Erythranthe peregrina . Sequencing confirmed that this species originated from  E. × robertsii , a sterile triploid hybrid between  E. guttata  and  E. lutea,  both of which have been introduced and naturalised in the United Kingdom. New populations of  E. peregrina  arose on  the Scottish mainland  and the  Orkney Islands  via genome duplication from local populations of  E. × robertsii . [ 5 ]  Because of a rare genetic mutation,  E. peregrina  is not sterile. [ 6 ]


On the other hand, polyploidization can also be a mechanism for a kind of 'reverse speciation', [ 7 ]  whereby gene flow is enabled following the polyploidy event, even between lineages that previously experienced no gene flow as diploids. This has been detailed at the genomic level in  Arabidopsis arenosa  and  Arabidopsis lyrata . [ 8 ]  Each of these species experienced independent autopolyploidy events (within-species polyploidy, described below), which then enabled subsequent interspecies gene flow of adaptive alleles, in this case stabilising each young polyploid lineage. [ 9 ]  Such polyploidy-enabled adaptive introgression may allow polyploids at act as 'allelic sponges', whereby they accumulate cryptic genomic variation that may be recruited upon encountering later environmental challenges. [ 10 ]


Polyploid  types are labeled according to the number of chromosome sets in the  nucleus . The letter  x  is used to represent the number of chromosomes in a single set:


Autopolyploids  are polyploids with multiple chromosome sets derived from a single  taxon .


Two examples of natural autopolyploids are the piggyback plant,  Tolmiea menzisii [ 19 ]  and the white sturgeon,  Acipenser transmontanum . [ 20 ]  Most instances of autopolyploidy result from the fusion of unreduced (2 n ) gametes, which results in either triploid ( n  + 2 n  = 3 n ) or tetraploid (2 n  + 2 n  = 4 n ) offspring. [ 21 ]  Triploid offspring are typically sterile (as in the phenomenon of  triploid block ), but in some cases they may produce high proportions of unreduced gametes and thus aid the formation of tetraploids. This pathway to tetraploidy is referred to as the  triploid bridge . [ 21 ]  Triploids may also persist through  asexual reproduction . In fact, stable autotriploidy in plants is often associated with  apomictic  mating systems. [ 22 ]  In agricultural systems, autotriploidy can result in seedlessness, as in  watermelons  and  bananas . [ 23 ]  Triploidy is also utilized in salmon and trout farming to induce sterility. [ 24 ] [ 25 ]


Rarely, autopolyploids arise from spontaneous, somatic genome doubling, which has been observed in apple ( Malus domesticus )  bud sports . [ 26 ]  This is also the most common pathway of artificially induced polyploidy, where methods such as  protoplast fusion  or treatment with  colchicine ,  oryzalin  or  mitotic inhibitors  are used to disrupt normal  mitotic  division, which results in the production of polyploid cells. This process can be useful in plant breeding, especially when attempting to introgress germplasm across ploidal levels. [ 27 ]


Autopolyploids possess at least three  homologous chromosome  sets, which can lead to high rates of multivalent pairing during  meiosis  (particularly in recently formed autopolyploids, also known as neopolyploids) and an associated decrease in fertility due to the production of  aneuploid  gametes. [ 28 ]  Natural or artificial selection for fertility can quickly stabilize meiosis in autopolyploids by restoring bivalent pairing during meiosis. Rapid adaptive evolution of the meiotic machinery, resulting in reduced levels of multivalents (and therefore stable autopolyploid meiosis) has been documented in  Arabidopsis arenosa [ 29 ]  and  Arabidopsis lyrata , [ 30 ]  with specific adaptive alleles of these species shared between only the evolved polyploids. [ 31 ] [ 32 ]


The high degree of  homology  among duplicated chromosomes causes autopolyploids to display  polysomic inheritance . [ 33 ]  This trait is often used as a diagnostic criterion to distinguish autopolyploids from allopolyploids, which commonly display disomic inheritance after they progress past the neopolyploid stage. [ 34 ]  While most polyploid species are unambiguously characterized as either autopolyploid or allopolyploid, these categories represent the ends of a spectrum of divergence between parental subgenomes. Polyploids that fall between these two extremes, which are often referred to as segmental allopolyploids, may display intermediate levels of polysomic inheritance that vary by locus. [ 35 ] [ 36 ]


About half of all polyploids are thought to be the result of autopolyploidy, [ 37 ] [ 38 ]  although many factors make this proportion hard to estimate. [ 39 ]


Allopolyploids  or  amphipolyploids  or  heteropolyploids  are polyploids with chromosomes derived from two or more diverged taxa.


As in autopolyploidy, this primarily occurs through the fusion of unreduced (2 n ) gametes, which can take place before or after  hybridization . In the former case, unreduced gametes from each diploid taxon – or reduced gametes from two autotetraploid taxa – combine to form allopolyploid offspring. In the latter case, one or more diploid  F 1  hybrids  produce unreduced gametes that fuse to form allopolyploid progeny. [ 40 ]  Hybridization followed by genome duplication may be a more common path to allopolyploidy because F 1  hybrids between taxa often have relatively high rates of unreduced gamete formation – divergence between the genomes of the two taxa result in abnormal pairing between  homoeologous  chromosomes or  nondisjunction  during meiosis. [ 40 ]  In this case, allopolyploidy can actually restore normal,  bivalent  meiotic pairing by providing each homoeologous chromosome with its own homologue. If divergence between homoeologous chromosomes is even across the two subgenomes, this can theoretically result in rapid restoration of bivalent pairing and disomic inheritance following allopolyploidization. However multivalent pairing is common in many recently formed allopolyploids, so it is likely that the majority of meiotic stabilization occurs gradually through selection. [ 28 ] [ 34 ]


Because pairing between homoeologous chromosomes is rare in established allopolyploids, they may benefit from fixed  heterozygosity  of homoeologous alleles. [ 41 ]  In certain cases, such heterozygosity can have beneficial  heterotic  effects, either in terms of fitness in natural contexts or desirable traits in agricultural contexts. This could partially explain the prevalence of allopolyploidy among crop species. Both bread  wheat  and  triticale  are examples of an allopolyploids with six chromosome sets.  Cotton ,  peanut , and  quinoa  are allotetraploids with multiple origins. In  Brassicaceous  crops, the  Triangle of U  describes the relationships between the three common diploid Brassicas ( B. oleracea ,  B. rapa ,  and  B. nigra ) and three allotetraploids ( B. napus ,  B. juncea ,  and  B. carinata ) derived from hybridization among the diploid species. A similar relationship exists between three diploid species of  Tragopogon  ( T. dubius ,  T. pratensis ,  and  T. porrifolius ) and two allotetraploid species ( T. mirus  and  T. miscellus ). [ 42 ]  Complex patterns of allopolyploid evolution have also been observed in animals, as in the frog genus  Xenopus . [ 43 ]


Organisms in which a particular chromosome, or chromosome segment, is under- or over-represented are said to be  aneuploid  (from the Greek words meaning "not", "good", and "fold"). Aneuploidy refers to a numerical change in part of the chromosome set, whereas polyploidy refers to a numerical change in the whole set of chromosomes. [ 44 ]


Polyploidy occurs in some tissues of animals that are otherwise diploid, such as human  muscle  tissues. [ 45 ]  This is known as  endopolyploidy . Species whose cells do not have nuclei, that is,  prokaryotes , may be polyploid, as seen in the large  bacterium   Epulopiscium fishelsoni . [ 46 ]  Hence  ploidy  is defined with respect to a cell.


A monoploid has only one set of chromosomes and the term is usually only applied to cells or organisms that are normally diploid. The more general term for such organisms is  haploid .


A polyploid that is newly formed.


That has become polyploid in more recent history; it is not as new as a neopolyploid and not as old as a paleopolyploid. It is a middle aged polyploid. Often this refers to whole genome duplication followed by intermediate levels of diploidization.


Ancient genome duplications probably occurred in the evolutionary history of all life. Duplication events that occurred long ago in the history of various  evolutionary lineages  can be difficult to detect because of subsequent  diploidization  (such that a polyploid starts to behave cytogenetically as a diploid over time) as  mutations  and gene translations gradually make one copy of each chromosome unlike the other copy. Over time, it is also common for duplicated copies of genes to accumulate mutations and become inactive pseudogenes. [ 47 ]


In many cases, these events can be inferred only through comparing  sequenced genomes . Examples of unexpected but recently confirmed ancient genome duplications include  baker's yeast  ( Saccharomyces cerevisiae ), mustard weed/thale cress ( Arabidopsis thaliana ),  rice  ( Oryza sativa ), and two rounds of whole genome duplication (the  2R hypothesis ) in an early  evolutionary   ancestor  of the  vertebrates  (which includes the  human  lineage) and another near the origin of the  teleost   fishes . [ 48 ]   Angiosperms  ( flowering plants ) have paleopolyploidy in their ancestry. All  eukaryotes  probably have experienced a polyploidy event at some point in their evolutionary history.


A karyotype is the characteristic chromosome complement of a  eukaryote   species . [ 49 ] [ 50 ]  The preparation and study of karyotypes is part of  cytology  and, more specifically,  cytogenetics .


Although the replication and transcription of DNA is highly standardized in  eukaryotes , the same cannot be said for their karyotypes, which are highly variable between species in chromosome number and in detailed organization despite being constructed out of the same macromolecules. In some cases, there is even significant variation within species. This variation provides the basis for a range of studies in what might be called evolutionary cytology.


Homoeologous chromosomes  are those brought together following  inter-species hybridization  and  allopolyploidization , and whose relationship was completely homologous in an ancestral species. For example,  durum wheat  is the result of the inter-species hybridization of two diploid grass species  Triticum urartu  and  Aegilops speltoides . Both diploid ancestors had two sets of 7 chromosomes, which were similar in terms of size and genes contained on them. Durum wheat contains a  hybrid genome  with two sets of chromosomes derived from  Triticum urartu  and two sets of chromosomes derived from  Aegilops speltoides . Each chromosome pair derived from the  Triticum urartu  parent is  homoeologous  to the opposite chromosome pair derived from the  Aegilops speltoides  parent, though each chromosome pair unto itself is  homologous .


Examples in animals are more common in non-vertebrates [ 51 ]  such as  flatworms ,  leeches , and  brine shrimp . Within vertebrates, examples of stable polyploidy include the  salmonids  and many  cyprinids  (i.e.  carp ). [ 52 ]  Some fish have as many as 400 chromosomes. [ 52 ]  Polyploidy also occurs commonly in amphibians; for example the biomedically important genus  Xenopus  contains many different species with as many as 12 sets of chromosomes (dodecaploid). [ 53 ]  Polyploid lizards are also quite common. Most are sterile and reproduce by  parthenogenesis ; [ citation needed ]  others, like  Liolaemus chiliensis , maintain sexual reproduction. Polyploid  mole salamanders  (mostly triploids) are all female and reproduce by  kleptogenesis , [ 54 ]  "stealing"  spermatophores  from diploid males of related species to trigger egg development but not incorporating the males' DNA into the offspring.


While some tissues of mammals, such as  parenchymal  liver cells, are polyploid, [ 55 ] [ 56 ]  rare instances of polyploid  mammals  are known, but most often result in  prenatal  death. An  octodontid   rodent  of  Argentina 's harsh  desert  regions, known as the  plains viscacha rat  ( Tympanoctomys barrerae ) has been reported as an exception to this 'rule'. [ 57 ]  However, careful analysis using chromosome paints shows that there are only two copies of each chromosome in  T. barrerae , not the four expected if it were truly a tetraploid. [ 58 ]  This rodent is not a  rat , but kin to  guinea pigs  and  chinchillas . Its "new" diploid (2 n ) number is 102 and so its cells are roughly twice normal size. Its closest living relation is  Octomys mimax , the  Andean  Viscacha-Rat of the same family, whose 2 n  = 56. It was therefore surmised that an  Octomys -like ancestor produced tetraploid (i.e., 2 n  = 4 x  = 112) offspring that were, by virtue of their doubled chromosomes, reproductively isolated from their parents.


Polyploidy was induced in fish by  Har Swarup  (1956) using a cold-shock treatment of the eggs close to the time of fertilization, which produced triploid embryos that successfully matured. [ 59 ] [ 60 ]  Cold or heat shock has also been shown to result in unreduced amphibian gametes, though this occurs more commonly in eggs than in sperm. [ 61 ]   John Gurdon  (1958) transplanted intact nuclei from somatic cells to produce diploid eggs in the frog,  Xenopus  (an extension of the work of Briggs and King in 1952) that were able to develop to the tadpole stage. [ 62 ]  The British scientist  J. B. S. Haldane  hailed the work for its potential medical applications and, in describing the results, became one of the first to use the word " clone " in reference to animals. Later work by  Shinya Yamanaka  showed how mature cells can be reprogrammed to become pluripotent, extending the possibilities to non-stem cells. Gurdon and Yamanaka were jointly awarded the Nobel Prize in 2012 for this work. [ 62 ]


True polyploidy rarely occurs in humans, although polyploid cells occur in highly  differentiated  tissue, such as liver  parenchyma , heart muscle, placenta and in bone marrow. [ 63 ] [ 64 ]   Aneuploidy  is more common.


Polyploidy occurs in humans in the form of  triploidy , with 69 chromosomes (sometimes called 69, XXX), and tetraploidy with 92 chromosomes (sometimes called 92, XXXX). Triploidy, usually due to  polyspermy , occurs in about 2–3% of all human pregnancies and ~15% of miscarriages. [ citation needed ]  The vast majority of triploid conceptions end as a  miscarriage ; those that do survive to term typically die shortly after birth. In some cases, survival past birth may be extended if there is  mixoploidy  with both a  diploid  and a triploid cell population present. There has been one report of a child surviving to the age of seven months with complete triploidy syndrome. He failed to exhibit normal mental or physical neonatal development, and died from a  Pneumocystis carinii  infection, which indicates a weak immune system. [ 65 ]


Triploidy may be the result of either  digyny  (the extra haploid set is from the mother) or  diandry  (the extra haploid set is from the father). Diandry is mostly caused by reduplication of the paternal haploid set from a single sperm, but may also be the consequence of dispermic (two sperm)  fertilization  of the egg. [ 66 ]  Digyny is most commonly caused by either failure of one meiotic division during oogenesis leading to a diploid  oocyte  or failure to extrude one  polar body  from the  oocyte . Diandry appears to predominate among early  miscarriages , while digyny predominates among triploid zygotes that survive into the fetal period. [ 67 ]  However, among early miscarriages, digyny is also more common in those cases less than  8 + 1 ⁄ 2  weeks gestational age or those in which an embryo is present. There are also two distinct  phenotypes  in triploid  placentas  and  fetuses  that are dependent on the origin of the extra  haploid  set. In digyny, there is typically an asymmetric poorly grown  fetus , with marked  adrenal   hypoplasia  and a very small  placenta . [ 68 ]  In diandry, a partial  hydatidiform mole  develops. [ 66 ]  These parent-of-origin effects reflect the effects of  genomic imprinting . [ citation needed ]


Complete tetraploidy is more rarely diagnosed than triploidy, but is observed in 1–2% of early miscarriages. However, some tetraploid cells are commonly found in chromosome analysis at  prenatal diagnosis  and these are generally considered 'harmless'. It is not clear whether these tetraploid cells simply tend to arise during  in vitro  cell culture or whether they are also present in placental cells  in vivo . There are, at any rate, very few clinical reports of fetuses/infants diagnosed with tetraploidy mosaicism.


Mixoploidy  is quite commonly observed in human preimplantation embryos and includes haploid/diploid as well as diploid/tetraploid mixed cell populations. It is unknown whether these embryos fail to implant and are therefore rarely detected in ongoing pregnancies or if there is simply a selective process favoring the diploid cells.


A polyploidy event occurred within the stem lineage of the  teleost  fish. [ 48 ]


Polyploidy is frequent in plants, some estimates suggesting that 30–80% of living plant species are polyploid, and many lineages show evidence of ancient polyploidy ( paleopolyploidy ) in their genomes. [ 69 ] [ 70 ] [ 71 ] [ 72 ]  Huge explosions in  angiosperm  species diversity appear to have coincided with the timing of ancient genome duplications shared by many species. [ 73 ]  It has been established that 15% of angiosperm and 31% of fern  speciation  events are accompanied by ploidy increase. [ 74 ]


Polyploid plants can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2 n ) gametes. [ 41 ]  Both autopolyploids (e.g. potato [ 75 ] ) and allopolyploids (such as canola, wheat and cotton) can be found among both wild and domesticated plant species.


Most polyploids display novel variation or morphologies relative to their parental species, that may contribute to the processes of  speciation  and eco-niche exploitation. [ 70 ] [ 41 ]  The mechanisms leading to novel variation in newly formed allopolyploids may include gene dosage effects (resulting from more numerous copies of genome content), the reunion of divergent gene regulatory hierarchies, chromosomal rearrangements, and  epigenetic  remodeling, all of which affect gene content and/or expression levels. [ 76 ] [ 77 ] [ 78 ] [ 79 ]  Many of these rapid changes may contribute to reproductive isolation and speciation. However, seed generated from  interploidy crosses , such as between polyploids and their parent species, usually have aberrant endosperm development which impairs their viability, [ 80 ] [ 81 ]  thus contributing to  polyploid speciation . Polyploids may also interbreed with diploids and produce polyploid seeds, as observed in the agamic complexes of  Crepis . [ 82 ]


Some plants are triploid. As  meiosis  is disturbed, these plants are sterile, with all plants having the same genetic constitution: Among them, the exclusively vegetatively propagated  saffron crocus  ( Crocus sativus ). Also, the extremely rare Tasmanian shrub  Lomatia tasmanica  is a triploid sterile species.


There are few naturally occurring polyploid  conifers . [ 83 ]  One example is the Coast Redwood  Sequoia sempervirens , which is a hexaploid (6 x ) with 66 chromosomes (2 n  = 6 x  = 66), although the origin is unclear. [ 84 ]